From David.Bauer at SCHERING.DE Mon Aug 1 02:36:46 2005 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Mon, 1 Aug 2005 08:36:46 +0200 Subject: [EMBOSS] Antwort: EMBOSS GUI problems In-Reply-To: Message-ID: Hi, I have installed the GUI last week and I can't reproduce this problem. water and needle with sequence pasted and uploaded from file run OK. Perl is 5.8.5 and Apache 1.3.26 on FreeBSD 4.9. David. emboss-bounces at emboss.open-bio.org schrieb am 30.07.2005 13:30:47: > Hi Luke and EMBOSS list > > I've installed the EMBOSS GUI and for the most part, it's working pretty > well. > > However for some apps (mainly seems to be alignment type ones like water, > needle, emma, but that may just be because I've tried more of them than > any others), it always fails > > Error: Unable to read sequence '' > Died: water terminated: Bad value for '-asequence' with -auto > defined > water exited with status 1... > > or in the /var/www/html/EMBOSS/runs/ error log, > > Error: Unable to read sequence '' > Died: water terminated: Bad value for '-asequence' with -auto defined > water exited with status 1... > > It doesn't seem to matter if it's sequence data pasted in, or uploaded > from a file. > > Some apps work fine, so I'm guessing it's not a fundamental problem like > permissions on a temp directory or something. > > Are you able to point me at where to start lookng ? > > Thanks, > Andrew > > > Animal Genetics and Genomics, PIRVic Attwood > 475 Mickleham Road, Attwood, 3049 > ph +61 3 92174342 > mob 0413 009 761 > > > ---------------- > There are 10 kinds of people...those who understand binary and those who > don't. > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss From pmr at ebi.ac.uk Mon Aug 1 05:05:00 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 01 Aug 2005 10:05:00 +0100 Subject: [EMBOSS] EMBOSS GUI problems In-Reply-To: References: Message-ID: <42EDE5BC.3070400@ebi.ac.uk> Andrew.Mather at dpi.vic.gov.au wrote: > Error: Unable to read sequence '' > Died: water terminated: Bad value for '-asequence' with -auto defined > water exited with status 1... This looks like what I would expect if there is no value for -asequence on the command line generated by EMBOSS::GUI. Luke ... over to you. Peter From Andrew.Mather at dpi.vic.gov.au Mon Aug 1 06:16:40 2005 From: Andrew.Mather at dpi.vic.gov.au (Andrew.Mather at dpi.vic.gov.au) Date: Mon, 1 Aug 2005 20:16:40 +1000 Subject: [EMBOSS] EMBOSS GUI problems Message-ID: Hi Peter, Yeah, that's what I figured too, but what's confused me is that it works for some apps, but not others. I guess I've assumed that something like getting the input sequence would be common to all apps but if it's not, that could explain some things. Andrew Animal Genetics and Genomics, PIRVic Attwood 475 Mickleham Road, Attwood, 3049 ph +61 3 92174342 mob 0413 009 761 ---------------- There are 10 kinds of people...those who understand binary and those who don't. pmr at ebi.ac.uk 01/08/05 07:05 PM To: Andrew.Mather at dpi.vic.gov.au cc: mcarthy at cs.usask.ca, emboss at emboss.open-bio.org Subject: Re: [EMBOSS] EMBOSS GUI problems Andrew.Mather at dpi.vic.gov.au wrote: > Error: Unable to read sequence '' > Died: water terminated: Bad value for '-asequence' with -auto defined > water exited with status 1... This looks like what I would expect if there is no value for -asequence on the command line generated by EMBOSS::GUI. Luke ... over to you. Peter From pmr at ebi.ac.uk Mon Aug 1 06:40:36 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 01 Aug 2005 11:40:36 +0100 Subject: [EMBOSS] EMBOSS GUI problems In-Reply-To: References: Message-ID: <42EDFC24.2010406@ebi.ac.uk> Andrew.Mather at dpi.vic.gov.au wrote: > Hi Peter, > > Yeah, that's what I figured too, but what's confused me is that it works > for some apps, but not others. > > I guess I've assumed that something like getting the input sequence would > be common to all apps but if it's not, that could explain some things. There are some dependiencies in the inputs for water and needle (both sequences must be protein or DNA) so they may have different processing. But emma has only one sequence input so that does not seem to be the common factor. Luke's address in your mail didn't work for me. I've copied this to another address for him (lukem at gene.pbi.nrc.ca). Peter > pmr at ebi.ac.uk > 01/08/05 07:05 PM > > > To: Andrew.Mather at dpi.vic.gov.au > cc: mcarthy at cs.usask.ca, emboss at emboss.open-bio.org > Subject: Re: [EMBOSS] EMBOSS GUI problems > > > Andrew.Mather at dpi.vic.gov.au wrote: > > >>Error: Unable to read sequence '' >>Died: water terminated: Bad value for '-asequence' with -auto defined >>water exited with status 1... > > > This looks like what I would expect if there is no value for -asequence on > the > command line generated by EMBOSS::GUI. > > Luke ... over to you. > > Peter > > > > From pmr at ebi.ac.uk Mon Aug 1 11:49:26 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 01 Aug 2005 16:49:26 +0100 Subject: [EMBOSS] Using seqret to fetch from .nal index databases In-Reply-To: <5C75DDA3-04A4-4A58-B925-31F9F017D8C4@uidaho.edu> References: <5C75DDA3-04A4-4A58-B925-31F9F017D8C4@uidaho.edu> Message-ID: <42EE4486.50302@ebi.ac.uk> Audra Johnson wrote: > Apologies for the length, but I want to be thorough. I'm doing blast > searches and then trying to fetch the sequences from the our genembl > database using seqret. For example: > > blastall -p tblastn /gcgdata_10.3/gcgblast/genembl -i > dp00061_disordered_115_168.fasta > I've tried using a seqret just for the database name I'm giving > blastall, and specifically saying the genembl.nal file: > > $ seqret > Reads and writes (returns) sequences > Input sequence(s): /gcgdata_10.3/gcgblast/genembl.nal:HUMRPA70KD > Error: Unable to read sequence '/gcgdata_10.3/gcgblast/ > genembl.nal:HUMRPA70KD' EMBOSS cannot read blast database files directly. EMBOSS can read the old format index files produced by formatdb, but not the latest ones - we have not yet decoded the index format. If you still have the FASTA format file /gcgdata_10.3/gcgblast/genembl then you can index this file with dbifasta (or dbxfasta using the new beta version indexing) and define it as a database for seqret - of use it in seqret the way you aer trying to use the .nal file (but this will be slow as it has to read the file until it fins the entry). If you have the same database in GCG format you can index it with dbigcg (or dbxgcg). If you use dbigcg or dbxgcg you may be able to use the GB_PR "gcg" database names in EMBOSS, by reusing the dbigcg indices with different files selected or excluded. Let me know if you would like more hints on how to do any of these. regards, Peter Rice From lukem at gene.pbi.nrc.ca Tue Aug 2 15:23:39 2005 From: lukem at gene.pbi.nrc.ca (Luke McCarthy) Date: Tue, 02 Aug 2005 13:23:39 -0600 Subject: [EMBOSS] EMBOSS GUI problems In-Reply-To: References: Message-ID: <1123010619.11724.15.camel@incognito.invalid> On Sat, 2005-07-30 at 04:40, Andrew.Mather at dpi.vic.gov.au wrote: > However for some apps (mainly seems to be alignment type ones like water, > needle, emma, but that may just be because I've tried more of them than > any others), it always fails > > Error: Unable to read sequence '' > Died: water terminated: Bad value for '-asequence' with -auto > defined > water exited with status 1... Do all of the applications that are failing require sequence input? Do all applications that require sequence input fail? What version of EMBOSS are you using (you can run embossversion from the GUI to get the number...) This is a really strange problem because sequence input isn't treated any differently from other input. Can you run applications that require other input files that aren't sequences? abiview, for example? What is happening here is that there is no value being passed for the 'asequence' parameter. When the input form is generated, it should be generating a field for the 'asequence' parameter. So, assuming you've filled in that field before trying to submit the input form, this shouldn't happen. One thing that occurs to me is that the naming convention for sequence parameters changed at some point (they used to be called sequencea/sequenceb and are now called asequence/bsequence...) Is it possible that the GUI is finding older versions of the ACD files? From the error output, it's clear that the version of water being run is looking for a parameter called 'asequence', but if the GUI read an old version of the ACD file when it generated the input page and thinks the parameter is called 'sequencea', maybe that's the problem? You can look in the EMBOSS::GUI::Conf module (the install script will have told you where it was installed to) and check the values of $EMBOSS_PREFIX, $EMBOSS_BIN and $EMBOSS_ACDROOT to make sure it's using the binaries and ACD files from the same EMBOSS version. This is actually very unlikely, as the GUI looks at the ACD file when it's building the command line, too. So it would have to find one ACD file when it was building the input form, and a different ACD file when it tried to run the application. > Some apps work fine, so I'm guessing it's not a fundamental problem like > permissions on a temp directory or something. No, if the temporary directory wasn't writable, all applications would fail. If your EMBOSS server is publicly accessible, email me (at lukem at gene.pbi.nrc.ca) with the URL and I'll poke around and try to figure out what's going on. Cheers, Luke From shrish at ccmb.res.in Wed Aug 3 05:35:14 2005 From: shrish at ccmb.res.in (Shrish Tiwari) Date: Wed, 3 Aug 2005 16:05:14 +0630 Subject: [EMBOSS] (no subject) Message-ID: Hi! I was installing the latest version of EMBOSS 3.0 and noticed during the make command the following: creating yank Making all in test No suffix list Making all in data No suffix list ... What does this mean? Shrish ______________________________________________________________________ Dr. Shrish Tiwari, Scientist BIC, Centre for Cellular and Molecular Biology Uppal Road, Hyderabad - 500 007 Phone: 91-40-7192776 (work), 91-40-7156603 (home) email: shrish at ccmb.res.in ______________________________________________________________________ From ajb at ebi.ac.uk Wed Aug 3 06:54:36 2005 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Wed, 3 Aug 2005 11:54:36 +0100 (BST) Subject: [EMBOSS] suffix list message In-Reply-To: References: Message-ID: <32918.172.31.70.166.1123066476.squirrel@webmail.ebi.ac.uk> The suffix list message will happen with some versions/installations of 'make' and can be safely ignored. It generally means that no files with the extension .c, .cc, .C, .p, .f, .F, .r, .y, .l, .s, .S, et cetera can be found in a particular directory. So, the message will usually be given in directories with no source code (etc). HTH Alan Bleasby EBI From george.magklaras at biotek.uio.no Thu Aug 11 12:29:56 2005 From: george.magklaras at biotek.uio.no (George Magklaras) Date: Thu, 11 Aug 2005 18:29:56 +0200 Subject: [EMBOSS] EMBASSY on EMBOSS 3.0.0 on RHEL WS 4 Message-ID: <42FB7D04.3020005@biotek.uio.no> Hi, Note: I realize this is EMBASSY, but I thought about dropping a note to you folks, as I am sure it is very likely you have seen this. After compiling separately zlib (1.2.3), libpng (1.2.8) and gd (2.0.33), I did a flawless EMBOSS 3.0.0 installation, and most embassy packages also compile properly. However, make on the PHYLIP-3.6b package quits with the following error message in response to the configure and make: ./configure --prefix=/mn/biotin/site --with-pngdriver=/mn/biotin/site/lib then make and I get the error: . . . gcc -O2 -o fconsense consense.o cons.o phylip.o -L/mn/biotin/site/lib/lib -L/mn/biotin/site/lib /mn/biotin/site/lib/libnucleus.so /mn/biotin/site/lib/libajax.so /mn/biotin/site/lib/libplplot.so -L/usr/X11R6/lib /mn/biotin/site/lib/libgd.so -L/usr/lib -lXpm -lX11 /usr/lib/libjpeg.so -lfontconfig /usr/lib/libfreetype.so -lpng12 -lpng -lz -lm /mn/biotin/site/lib/libz.a(compress.o)(.text+0xa0): In function `compress': : multiple definition of `compress' cons.o(.text+0x4e0): first defined here /usr/bin/ld: Warning: size of symbol `compress' changed from 326 in cons.o to 163 in /mn/biotin/site/lib/libz.a(compress.o) As far as I can see, the config log indicates that the cmd line got the options and the relevant libraries were found: checking if png driver is wanted... yes checking for inflateEnd in -lz... yes checking for png_destroy_read_struct in -lpng... yes checking for gdImageCreateFromPng in -lgd... yes PNG libraries found My compiler is: biotin.uio.no# gcc -v Reading specs from /usr/lib/gcc/i386-redhat-linux/3.4.3/specs Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-java-awt=gtk --host=i386-redhat-linux Thread model: posix gcc version 3.4.3 20050227 (Red Hat 3.4.3-22.1) Is this a library mix and match problem, or do I need another compiler...or...? Best Regards, GM -- -- George B. Magklaras Senior Computer Systems Engineer/UNIX Systems Administrator The Biotechnology Centre of Oslo, University of Oslo http://www.biotek.uio.no/ EMBnet Norway: http://www.biotek.uio.no/EMBNET/ Tel: +47-22840535 -- From ajb at ebi.ac.uk Thu Aug 11 13:34:17 2005 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Thu, 11 Aug 2005 18:34:17 +0100 (BST) Subject: [EMBOSS] EMBASSY on EMBOSS 3.0.0 on RHEL WS 4 In-Reply-To: <42FB7D04.3020005@biotek.uio.no> References: <42FB7D04.3020005@biotek.uio.no> Message-ID: <34006.81.96.71.66.1123781657.squirrel@webmail.ebi.ac.uk> That's the first report we've had of that problem. All compilers we've tried have let that error pass and correctly guessed the meaning of the code. Nevertheless it is an error so thanks for reporting it. I have just put a replacement file as ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIP-3.6b.tar.gz for anyone who has experienced the same compilation problem. HTH Alan Bleasby EBI From jeremy at biochem.uthscsa.edu Thu Aug 11 14:27:05 2005 From: jeremy at biochem.uthscsa.edu (Jeremy Mann) Date: Thu, 11 Aug 2005 13:27:05 -0500 (CDT) Subject: [EMBOSS] Difficulty with login Message-ID: <46012.129.111.174.49.1123784825.squirrel@biochem.uthscsa.edu> I'm trying to setup a jemboss server for a few researchers here and I have a problem I can't find an answer too. For some reason I can't login with a valid user account. When I run the client in debug mode, I get: javax.net.ssl.SSLHandshakeException: sun.security.validator.ValidatorException: No trusted certificate found I can't find this in the documentation. What exactly do I need to do to get this "trusted certificate"?? Thanks.. -- Jeremy Mann jeremy at biochem.uthscsa.edu University of Texas Health Science Center Bioinformatics Core Facility http://www.bioinformatics.uthscsa.edu Phone: (210) 567-2672 From tjc at sanger.ac.uk Fri Aug 12 03:58:55 2005 From: tjc at sanger.ac.uk (Tim Carver) Date: Fri, 12 Aug 2005 08:58:55 +0100 Subject: [EMBOSS] Difficulty with login In-Reply-To: <46012.129.111.174.49.1123784825.squirrel@biochem.uthscsa.edu> Message-ID: Hi Jeremy There are a number of reasons why it may complain about authentication. Here are the common ones: 1. the jembossctl script is not set to root and chmod'ed u+s 2. the results directory is not world read-writable 3. the tomcat server is not being run with the same UID that was given to the installation script However, from the look of the error you get it seems unlikely to be these. If you select SSL/Https for the protocol then the install script creates client & server certificates. These are used when connecting to the server to validate with the SSL handshake. You should first check your tomcat logs to see if the server is complaining about not finding this ($TOMCAT/logs/catalina.out). This should give some clues as to why you get that exception. Regards Tim Carver On 11/8/05 7:27 pm, "Jeremy Mann" wrote: > I'm trying to setup a jemboss server for a few researchers here and I have > a problem I can't find an answer too. For some reason I can't login with a > valid user account. When I run the client in debug mode, I get: > > javax.net.ssl.SSLHandshakeException: > sun.security.validator.ValidatorException: No trusted certificate found > > I can't find this in the documentation. What exactly do I need to do to > get this "trusted certificate"?? > > Thanks.. > > From benys at usp.br Wed Aug 17 09:01:16 2005 From: benys at usp.br (Beny Spira) Date: Wed, 17 Aug 2005 10:01:16 -0300 Subject: [EMBOSS] EMBOSS explorer In-Reply-To: <1121980112.5376.11.camel@incognito.invalid> References: <1121980112.5376.11.camel@incognito.invalid> Message-ID: <200508171001.17220.benys@usp.br> Hi Luke I would like to install EMBOSS explorer for the first time. I downloaded the source, but it says it needs some CPAN modules. I found those modules but do not know how to use them. How to install the whole package or is there any basic literature to read about it? Thank you in advance, Beny > Hi everybody, > > I'm pleased to finally announce a new release of the EMBOSS interface > formerly known as EMBOSS::GUI, now known as EMBOSS explorer. > > Development has moved to SourceForge.net and the new home page for the > interface is http://embossgui.sourceforge.net/ It's quite spartan at > the moment, but I'll be adding a FAQ as questions are frequent asked > (and answered...) > > You can download EMBOSS explorer at > http://prdownloads.sourceforge.net/embossgui/emboss-explorer-2.0.0.tar.gz?d >ownload > > The new release has been tested against EMBOSS-3.0.0, but not > thoroughly. Please report bugs using the bug tracker at > http://sourceforge.net/tracker/?atid=699414&group_id=124389&func=browse > (as a last resort, email them to mccarthy at users.sourceforge.net, but I'm > hoping that use of the bug tracker will help with duplicate reports and > other organizational issues...) > > Cheers, > > Luke > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Beny Spira Departamento de Microbiologia Instituto de Ci?ncias Biom?dicas Universidade de S?o Paulo Av. Prof. Lineu Prestes 1374 S?o Paulo-SP CEP:05508-900 Tel: 5511-3091-7347 FAX: 5511-3091-7354 E-mail: benys at usp.br %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From yuichiyoshi at gmail.com Wed Aug 17 13:09:59 2005 From: yuichiyoshi at gmail.com (Yoshida Yuichi) Date: Thu, 18 Aug 2005 02:09:59 +0900 Subject: [EMBOSS] emboss.defaut to access the enspep Message-ID: Hi, everyone, There is the following descriptions in the document of showdb command (/usr/share/EMBOSS/doc/programs/text/showdb.txt) > % showdb > Displays information on the currently available databases > > # Name Type ID Qry All Comment > # ==== ==== == === === ======= > enspep P OK OK OK ENSEMBL pep > enspepp P OK OK OK ENSEMBL pep predicted But I can't access the enspep (ENSEMBL pep) and enspepp (ENSEMBL pep predicted) by the showdb command. How should I describe the emboss.default (or .embossrc) to be able to access the enspep and enspepp. Would you please show me how to write the emboss.defaut (or .embossrc) in my case? ----- Yuichi Yoshida From jison at ebi.ac.uk Thu Aug 18 02:57:45 2005 From: jison at ebi.ac.uk (Jon Ison) Date: Thu, 18 Aug 2005 07:57:45 +0100 (BST) Subject: [EMBOSS] emboss.defaut to access the enspep In-Reply-To: References: Message-ID: <40155.172.31.8.12.1124348265.squirrel@webmail.ebi.ac.uk> Dear Yuichi enspep and enspepp are just examples used in the showdb documentation. You would need to create a database definition in your 'emboss.default' file (or '.embossrc' in your home directory). Instructions are here: http://emboss.sourceforge.net/docs/themes/Databases.html Get back in touch if you get stuck. J:) > Hi, everyone, > > There is the following descriptions in the document of showdb > command (/usr/share/EMBOSS/doc/programs/text/showdb.txt) > >> % showdb >> Displays information on the currently available databases >> >> # Name Type ID Qry All Comment >> # ==== ==== == === === ======= >> enspep P OK OK OK ENSEMBL pep >> enspepp P OK OK OK ENSEMBL pep predicted > > But I can't access the enspep (ENSEMBL pep) and enspepp > (ENSEMBL pep predicted) by the showdb command. > > How should I describe the emboss.default (or .embossrc) to > be able to access the enspep and enspepp. > > Would you please show me how to write the emboss.defaut > (or .embossrc) in my case? > > ----- > Yuichi Yoshida > > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss > From jison at ebi.ac.uk Thu Aug 18 03:01:33 2005 From: jison at ebi.ac.uk (Jon Ison) Date: Thu, 18 Aug 2005 08:01:33 +0100 (BST) Subject: [EMBOSS] Yoshida Yuishi ... Message-ID: <40158.172.31.8.12.1124348493.squirrel@webmail.ebi.ac.uk> emboss at emboss.open-bio.org From pmr at ebi.ac.uk Thu Aug 18 05:30:29 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 18 Aug 2005 10:30:29 +0100 Subject: [EMBOSS] emboss.defaut to access the enspep In-Reply-To: References: Message-ID: <43045535.8040505@ebi.ac.uk> Yoshida Yuichi wrote: > Hi, everyone, > > There is the following descriptions in the document of showdb > command (/usr/share/EMBOSS/doc/programs/text/showdb.txt) > > >>% showdb >>Displays information on the currently available databases >> >># Name Type ID Qry All Comment >># ==== ==== == === === ======= >>enspep P OK OK OK ENSEMBL pep >>enspepp P OK OK OK ENSEMBL pep predicted > > > But I can't access the enspep (ENSEMBL pep) and enspepp > (ENSEMBL pep predicted) by the showdb command. > > How should I describe the emboss.default (or .embossrc) to > be able to access the enspep and enspepp. The current showdb.txt file does not use enspep or enspepp as databases. A little history ... We generate the showdb.txt file from EMBOSS documentation on the website http://emboss.sourceforge.net/apps/showdb.html for each release. The usage example and the example output are in turn generated from our QA test suite. Your installation's showdb.txt file may be from an old release of EMBOSS, before we started to build the files from sourceforge. The older versions of showdb.txt used the databases installed at HGMP/RFCGR, where the EMBOSS developers were working. This institute has now closed and the development has moved to all be at EBI. The showdb.txt file was updated a year ago in release 2.10.0 when we started to move files from the HGMP website to sourceforge. If I recall correctly, HGMP's enspep and enspepp databases pointed to their SRS server, which has also closed. The ENSPEP database can be defined (for single entries only) using the Sanger Centre's SRS server: DB enspep [ type: "N" method: "SRSWWW" format: "fasta" url: "http://srs.sanger.ac.uk/srs7bin/cgi-bin/wgetz" dbalias: "ensemblpep" comment: "ensembl pep" ] To define is for multiple entries, use "methodquery" instead of "method" - this will allow you to use wildcard IDs. There is a list of publicly available SRS servers at http://downloads.lionbio.co.uk/publicsrs.html (liked to the EBI server's fron page. I can find nothing to match HGMP's "enspepp" database - unless it was simply a duplicate of the enspep database with a different access method. Sadly, the HGMP SRS server had more databases than any other server in the world. Some of them were not available anywhere else. HGMP may have also indexed enspep and enspepp in some other way (with dbifasta or dbiflat), using the ENSEMBL flatfiles from ftp.ensembl.org for example ftp://ftp.ensembl.org/pub/current_human/data/fasta/pep/ (for FASTA format files) or ftp://ftp.ensembl.org/pub/current_human/data/embl/pep/ for "embl" format files. There are separate files for some species that HGMP may have used for their two databases enspep and enspepp. We are working on ways to generate more information from showdb so that we can find out more about the database definitions (for sites that still exist!) in a future release. Hope that helps Peter Rice From anders.nister at lcb.uu.se Thu Aug 18 10:46:03 2005 From: anders.nister at lcb.uu.se (Anders =?ISO-8859-1?Q?Nist=E9r?=) Date: Thu, 18 Aug 2005 14:46:03 +0000 Subject: [EMBOSS] emma/clustalw PATH problems Message-ID: <20050818144603.E409E1E8@colibri.its.uu.se> I am trying to run emma, and for certain reasons i don't have clustalw in my PATH. Running emma produces this error: EMBOSS An error in ajsys.c at line 398: cannot find program 'clustalw' Looking through the manual for emma there is a mention of EMBOSS_CLUSTALW: "cannot find program 'clustalw'" - means that the ClustalW program has not been set up on your site or is not in your environment (i.e. is not on your path). The solutions are to (1) install clustalw in the path so that emma can find it with the command "clustalw", or (2) define a variable (an environment variable of in emboss.defaults or your .embossrc file) called EMBOSS_CLUSTALW containing the command (program name or full path) to run clustalw if you have it elsewhere on your system. So I'm supposed to be able to specify the full path to clustalw through EMBOSS_CLUSTALW.... Setting this variable to the full path of clustalw produces a similar error to the one before. EMBOSS An error in ajsys.c at line 398: cannot find program '/usr/local/bin/clustalw' Looking through the emma source code I can see that ajSystemEnv is used to execute clustalw, this function will always look through the PATH env variable for the executable it is trying to run, so specifying a full path does absolutely nothing to get around the problem. Is the documentation wrong or is this a bug ? Has anyone got a workaround ? Is there any emboss function for executing an external program directly, without it being present in PATH ? /Anders Nist?r From george.magklaras at biotek.uio.no Thu Aug 18 11:15:57 2005 From: george.magklaras at biotek.uio.no (George Magklaras) Date: Thu, 18 Aug 2005 17:15:57 +0200 Subject: [EMBOSS] emma/clustalw PATH problems In-Reply-To: <20050818144603.E409E1E8@colibri.its.uu.se> References: <20050818144603.E409E1E8@colibri.its.uu.se> Message-ID: <4304A62D.6020408@biotek.uio.no> How about placing the clustalw binary ( I assume that you have compiled this separately) into the same directory where you have the emboss binaries? If every other aspect of your EMBOSS install is OK then that should work? GM -- -- George B. Magklaras Senior Computer Systems Engineer/UNIX Systems Administrator The Biotechnology Centre of Oslo, University of Oslo http://www.biotek.uio.no/ EMBnet Norway: http://www.biotek.uio.no/EMBNET/ Anders Nist?r wrote: >I am trying to run emma, and for certain reasons i don't have clustalw in my >PATH. > >Running emma produces this error: > > EMBOSS An error in ajsys.c at line 398: >cannot find program 'clustalw' > > >Looking through the manual for emma there is a mention of EMBOSS_CLUSTALW: > > "cannot find program 'clustalw'" - means that the ClustalW program has > not been set up on your site or is not in your environment (i.e. is > not on your path). The solutions are to (1) install clustalw in the > path so that emma can find it with the command "clustalw", or (2) > define a variable (an environment variable of in emboss.defaults or > your .embossrc file) called EMBOSS_CLUSTALW containing the command > (program name or full path) to run clustalw if you have it elsewhere > on your system. > >So I'm supposed to be able to specify the full path to clustalw through >EMBOSS_CLUSTALW.... > >Setting this variable to the full path of clustalw produces a similar error >to the one before. > > EMBOSS An error in ajsys.c at line 398: >cannot find program '/usr/local/bin/clustalw' > >Looking through the emma source code I can see that ajSystemEnv is used to >execute clustalw, this function will always look through the PATH env >variable for the executable it is trying to run, so specifying a full path >does absolutely nothing to get around the problem. > >Is the documentation wrong or is this a bug ? >Has anyone got a workaround ? >Is there any emboss function for executing an external program directly, >without it being present in PATH ? > >/Anders Nist?r > >_______________________________________________ >EMBOSS mailing list >EMBOSS at emboss.open-bio.org >http://newportal.open-bio.org/mailman/listinfo/emboss > > From gbottu at ben.vub.ac.be Thu Aug 18 11:30:20 2005 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Thu, 18 Aug 2005 17:30:20 +0200 Subject: [EMBOSS] emma/clustalw PATH problems In-Reply-To: <20050818144603.E409E1E8@colibri.its.uu.se> References: <20050818144603.E409E1E8@colibri.its.uu.se> Message-ID: <20050818153020.GA15471@bigben.ulb.ac.be> On Thu, Aug 18, 2005 at 02:46:03PM +0000, Anders Nist?r wrote: > I am trying to run emma, and for certain reasons i don't have clustalw in my > PATH. > How about placing the clustalw binary ( I assume that you have compiled > this separately) into the same directory where you have the emboss > binaries? I think the best is to put in the directory with the EMBOSS binaries a logical link pointing to clustalw. Note by the way that you also need a logical link to primer3_core to make eprimer3 work. Guy Bottu, Belgian EMBnet Node From anders.nister at lcb.uu.se Thu Aug 18 12:13:12 2005 From: anders.nister at lcb.uu.se (Anders =?ISO-8859-1?Q?Nist=E9r?=) Date: Thu, 18 Aug 2005 16:13:12 +0000 Subject: [EMBOSS] emma/clustalw PATH problems In-Reply-To: <4304A62D.6020408@biotek.uio.no> Message-ID: <20050818161312.4CBA71E8@colibri.its.uu.se> Den 8/18/2005, skrev "George Magklaras" : >How about placing the clustalw binary ( I assume that you have compiled >this separately) into the same directory where you have the emboss >binaries? If every other aspect of your EMBOSS install is OK then that >should work? > >GM Unfortunately the binaries already are in the same directory, I am calling emma with the full path from a Cocoa application (PATH is not set)... /Anders Nist?r From jeremy at biochem.uthscsa.edu Thu Aug 18 12:18:05 2005 From: jeremy at biochem.uthscsa.edu (Jeremy Mann) Date: Thu, 18 Aug 2005 11:18:05 -0500 (CDT) Subject: [EMBOSS] emboss server Message-ID: <39102.129.111.174.49.1124381885.squirrel@biochem.uthscsa.edu> I still have not found the cure to my login problems with the EMBOSS server. I've done the install several times now with and without encryption, different kinds of authentication and nothing seems to work. With encryption selected I get: No trusted certificate found I have done the encrypted install about a hundred times now and each time it does make the certificate and I have edited the server.xml to reflect the change. So I don't know what I'm missing here. Without encryption I don't get any errors, but the login prompt is always popping up. I've tried all 6 types of authentication and none of them work. I'm at my wits end and my head hurts from banging it on my desk ;) Could somebody with a working Linux EMBOSS server contact me off or on list? Thanks a bunch! System: Suse x86_64 9.1 Java 1.4.2 EMBOSS 3.0.0 Latest Jemboss client Tomcat 5.5.9 with compat library Axis 1_2 -- Jeremy Mann jeremy at biochem.uthscsa.edu University of Texas Health Science Center Bioinformatics Core Facility http://www.bioinformatics.uthscsa.edu Phone: (210) 567-2672 From pmr at ebi.ac.uk Thu Aug 18 13:13:04 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 18 Aug 2005 18:13:04 +0100 Subject: [EMBOSS] emma/clustalw PATH problems In-Reply-To: <20050818144603.E409E1E8@colibri.its.uu.se> References: <20050818144603.E409E1E8@colibri.its.uu.se> Message-ID: <4304C1A0.8040206@ebi.ac.uk> Anders Nist?r wrote: > Looking through the manual for emma there is a mention of EMBOSS_CLUSTALW: > > "cannot find program 'clustalw'" - means that the ClustalW program has > not been set up on your site or is not in your environment (i.e. is > not on your path). The solutions are to (1) install clustalw in the > path so that emma can find it with the command "clustalw", or (2) > define a variable (an environment variable of in emboss.defaults or > your .embossrc file) called EMBOSS_CLUSTALW containing the command > (program name or full path) to run clustalw if you have it elsewhere > on your system. > > So I'm supposed to be able to specify the full path to clustalw through > EMBOSS_CLUSTALW.... > > Is the documentation wrong or is this a bug ? Ouch. It is a bug. The variable was originally set to allow older or newer versions of clustalw to be called. We have not tested programs that are not in the path. I am sure we can find a workaround for a fully specified path to the program. regards, Peter From andrespinzon at gmail.com Thu Aug 18 13:46:08 2005 From: andrespinzon at gmail.com (Andres Pinzon) Date: Thu, 18 Aug 2005 12:46:08 -0500 Subject: [EMBOSS] emboss server In-Reply-To: <39102.129.111.174.49.1124381885.squirrel@biochem.uthscsa.edu> References: <39102.129.111.174.49.1124381885.squirrel@biochem.uthscsa.edu> Message-ID: <8968fc7e05081810462e89b78c@mail.gmail.com> 2005/8/18, Jeremy Mann : > I'm at my wits end and my head hurts from banging it on my desk ;) Could > somebody with a working Linux EMBOSS server contact me off or on list? Hi, I really dont know what you mean with an "EMBOSS server", what I actually have is a GNU/Linux webserver on top of which emboss runs. We have several wEMBOSS/EMBOSSGUI users as well as command line EMBOSS users via SSH. If I can help u please ask me. ;-) -- --------- Andr?s Pinz?n [http://www.andrespinzon.com] Bioinformatics Center, Colombia EMBnet node Biotechnology Institute - National University of Colombia http://bioinf.ibun.unal.edu.co Tel +57 3165000 ext 16961 Fax +571 3165415 ---------- From dalloliogm at fastwebnet.it Thu Aug 18 15:07:04 2005 From: dalloliogm at fastwebnet.it (Dall'Olio Giovanni) Date: Thu, 18 Aug 2005 21:07:04 +0200 Subject: [EMBOSS] transfac site.dat ftp address Message-ID: <42F8C5A800003F7F@ms003msg.mail.fw> Hi all, Pleased to know you, I'm a student of bioinformatics from Barcelona. I was trying to use the 'tfscan' tool, but I can't find an ftp server to download the 'site.dat' file that is required for this tool. I've searched in Internet with google but I've only found this, that seems to be down: http://transfac.gbf.de/cgi-bin/download/download.pl Someone can help me in any way? I will appreciate it a lot. Thank you! --------------------------------------------- Dall'Olio Giovanni Marco, studente di Biotecnologie all'Universit? di Bologna. puoi trovarmi anche all'indirizzo dalloliogm at gmail.it p.s. visita il mio sito!! www.dalloliogm.tk (o http://dalloliogm.altervista.org) questo haiku e' dedicato a tutti coloro che ancora usano Windows: A file that big? It might be very useful. But now it is gone. -- David J. Liszewski Un file cos? grande? / Poteva esserti molto utile. / Ma adesso non c'? pi? http://digilander.libero.it/bunix/haiku.html From golharam at umdnj.edu Thu Aug 18 15:10:52 2005 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 18 Aug 2005 15:10:52 -0400 Subject: [EMBOSS] emma/clustalw PATH problems In-Reply-To: <4304C1A0.8040206@ebi.ac.uk> Message-ID: <00ea01c5a428$8da8bc60$2f01a8c0@GOLHARMOBILE1> I ran into the same problem. I simply moved clustalw into a directory in my path and everything works okay... -----Original Message----- From: emboss-bounces at emboss.open-bio.org [mailto:emboss-bounces at emboss.open-bio.org] On Behalf Of Peter Rice Sent: Thursday, August 18, 2005 1:13 PM To: Anders Nist?r Cc: emboss at emboss.open-bio.org Subject: Re: [EMBOSS] emma/clustalw PATH problems Anders Nist?r wrote: > Looking through the manual for emma there is a mention of > EMBOSS_CLUSTALW: > > "cannot find program 'clustalw'" - means that the ClustalW program has > not been set up on your site or is not in your environment (i.e. is > not on your path). The solutions are to (1) install clustalw in the > path so that emma can find it with the command "clustalw", or (2) > define a variable (an environment variable of in emboss.defaults or > your .embossrc file) called EMBOSS_CLUSTALW containing the command > (program name or full path) to run clustalw if you have it elsewhere > on your system. > > So I'm supposed to be able to specify the full path to clustalw > through EMBOSS_CLUSTALW.... > > Is the documentation wrong or is this a bug ? Ouch. It is a bug. The variable was originally set to allow older or newer versions of clustalw to be called. We have not tested programs that are not in the path. I am sure we can find a workaround for a fully specified path to the program. regards, Peter _______________________________________________ EMBOSS mailing list EMBOSS at emboss.open-bio.org http://newportal.open-bio.org/mailman/listinfo/emboss From andrespinzon at gmail.com Thu Aug 18 15:20:09 2005 From: andrespinzon at gmail.com (Andres Pinzon) Date: Thu, 18 Aug 2005 14:20:09 -0500 Subject: [EMBOSS] transfac site.dat ftp address In-Reply-To: <42F8C5A800003F7F@ms003msg.mail.fw> References: <42F8C5A800003F7F@ms003msg.mail.fw> Message-ID: <8968fc7e0508181220230e456b@mail.gmail.com> 2005/8/18, Dall'Olio Giovanni : > I was trying to use the 'tfscan' tool, but I can't find an ftp server to > download the 'site.dat' file that is required for this tool. Hi, as far as I know you are not supossed to download the database,(unless you are doing your own EMBOSS installation) you just have to define an input file and run the tool, thats it. The server which runs the tool should have the database already installed. Am I wrong? -- --------- Andr?s Pinz?n [http://www.andrespinzon.com] Bioinformatics Center, Colombia EMBnet node Biotechnology Institute - National University of Colombia http://bioinf.ibun.unal.edu.co Tel +57 3165000 ext 16961 Fax +571 3165415 ---------- From ajb at ebi.ac.uk Thu Aug 18 16:07:19 2005 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Thu, 18 Aug 2005 21:07:19 +0100 (BST) Subject: [EMBOSS] transfac site.dat ftp address In-Reply-To: <42F8C5A800003F7F@ms003msg.mail.fw> References: <42F8C5A800003F7F@ms003msg.mail.fw> Message-ID: <39657.81.96.71.66.1124395639.squirrel@webmail.ebi.ac.uk> The last free public version of transfac is on ftp://ftp.ebi.ac.uk/pub/databases/transfac/ (from memory) You can use the site.dat from that, write your own local version or pay the transfac people for the latest data. HTH Alan Bleasby EBI From emilywxu at yahoo.ca Thu Aug 18 19:28:11 2005 From: emilywxu at yahoo.ca (emily xu) Date: Thu, 18 Aug 2005 19:28:11 -0400 (EDT) Subject: [EMBOSS] needle qualifier Message-ID: <20050818232811.67700.qmail@web34011.mail.mud.yahoo.com> Hi there, I am new user and just installed the EMBOSS3.0.0 on UNIX. However, when I was trying to run program needle, I got the following error: UNIX % emboss/needle Needleman-Wunsch global alignment. Input sequence: query.1 Second sequence(s): target.1 Gap opening penalty [10.0]: 10.0 Gap extension penalty [0.5]: 0.5 Output alignment [ftsh_ecoli.needle]: ftsh_ecoli.needle Died: Qualifier '-bsequence' not found Why is it looking for '-bsequence'? The second sequence(s) have already been entered. Could someone help me with this? Thanks very much! Emily __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From David.Bauer at SCHERING.DE Fri Aug 19 01:34:42 2005 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Fri, 19 Aug 2005 07:34:42 +0200 Subject: [EMBOSS] Antwort: needle qualifier In-Reply-To: <20050818232811.67700.qmail@web34011.mail.mud.yahoo.com> Message-ID: I had a similar problem on a machine with some very old emboss libs hanging around. (in former time the parameter was named sequenceb and not bsequence) Make sure that you have only the current libajax, libajaxg and libnucleus in your search path for dynamic libraries. David. emboss-bounces at emboss.open-bio.org schrieb am 19/08/2005 01:28:11: > Hi there, > > I am new user and just installed the EMBOSS3.0.0 on > UNIX. However, when I was trying to run program > needle, I got the following error: > > UNIX % emboss/needle > Needleman-Wunsch global alignment. > Input sequence: query.1 > Second sequence(s): target.1 > Gap opening penalty [10.0]: 10.0 > Gap extension penalty [0.5]: 0.5 > Output alignment [ftsh_ecoli.needle]: > ftsh_ecoli.needle > Died: Qualifier '-bsequence' not found > > Why is it looking for '-bsequence'? The second > sequence(s) have already been entered. > Could someone help me with this? Thanks very much! > > Emily > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss From Sean.Maceachern at dpi.vic.gov.au Thu Aug 18 19:01:53 2005 From: Sean.Maceachern at dpi.vic.gov.au (Sean.Maceachern at dpi.vic.gov.au) Date: Fri, 19 Aug 2005 09:01:53 +1000 Subject: [EMBOSS] emma/clustalw PATH problems Message-ID: I have had a simillar problem with eprimer3, a temporary fix will be to modify your path so that it can find the clustalw binary eg) export PATH=$PATH:/home/sm82/primer3_1.0.0/src anders.nister at lcb.uu.se Sent by: To: emboss at emboss.open-bio.org emboss-bounces at emboss.o cc: pen-bio.org Subject: [EMBOSS] emma/clustalw PATH problems 19/08/2005 12:46 AM I am trying to run emma, and for certain reasons i don't have clustalw in my PATH. Running emma produces this error: EMBOSS An error in ajsys.c at line 398: cannot find program 'clustalw' Looking through the manual for emma there is a mention of EMBOSS_CLUSTALW: "cannot find program 'clustalw'" - means that the ClustalW program has not been set up on your site or is not in your environment (i.e. is not on your path). The solutions are to (1) install clustalw in the path so that emma can find it with the command "clustalw", or (2) define a variable (an environment variable of in emboss.defaults or your .embossrc file) called EMBOSS_CLUSTALW containing the command (program name or full path) to run clustalw if you have it elsewhere on your system. So I'm supposed to be able to specify the full path to clustalw through EMBOSS_CLUSTALW.... Setting this variable to the full path of clustalw produces a similar error to the one before. EMBOSS An error in ajsys.c at line 398: cannot find program '/usr/local/bin/clustalw' Looking through the emma source code I can see that ajSystemEnv is used to execute clustalw, this function will always look through the PATH env variable for the executable it is trying to run, so specifying a full path does absolutely nothing to get around the problem. Is the documentation wrong or is this a bug ? Has anyone got a workaround ? Is there any emboss function for executing an external program directly, without it being present in PATH ? /Anders Nist?r _______________________________________________ EMBOSS mailing list EMBOSS at emboss.open-bio.org http://newportal.open-bio.org/mailman/listinfo/emboss From ajb at ebi.ac.uk Fri Aug 19 05:15:48 2005 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Fri, 19 Aug 2005 10:15:48 +0100 (BST) Subject: [EMBOSS] needle qualifier In-Reply-To: <20050818232811.67700.qmail@web34011.mail.mud.yahoo.com> References: <20050818232811.67700.qmail@web34011.mail.mud.yahoo.com> Message-ID: <48138.81.96.71.66.1124442948.squirrel@webmail.ebi.ac.uk> To expand on the old library version issue: as of EMBOSS 3.0.0 we've started naming the ajax, ajaxg and nucleus libraries after the release number. So, the current library files will be called (e.g.) libajax.so.3.0.0 and there'll be symbolic links of libajax.so.3 and libajax.so to it. Any older libraries would probably be called (e.g.) libajax.so.1.0.0 or somesuch. HTH Alan From gbottu at ben.vub.ac.be Fri Aug 19 09:16:38 2005 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Fri, 19 Aug 2005 15:16:38 +0200 Subject: [EMBOSS] transfac site.dat ftp address In-Reply-To: <42F8C5A800003F7F@ms003msg.mail.fw> References: <42F8C5A800003F7F@ms003msg.mail.fw> Message-ID: <20050819131638.GA23671@bigben.ulb.ac.be> The file in the ftp server of the EBI is the last one that you could download just like that. If you like I can send you a copy of the site.dat version 4.0, less old but still from march 2000. This was the last academic users could get after signing a licence. In the mean time the ftp site has vanished and I do not think they will mind that I send you a copy, since it is still a very old file. The up-to-date version of TRANSFAC is only available against payment and not in the format suitable for standard EMBOSS and SRS. Regards, Guy Bottu, Belgian EMBnet Node From Andrew.Mather at dpi.vic.gov.au Fri Aug 19 21:38:24 2005 From: Andrew.Mather at dpi.vic.gov.au (Andrew.Mather at dpi.vic.gov.au) Date: Sat, 20 Aug 2005 11:38:24 +1000 Subject: [EMBOSS] emma/clustalw PATH problems Message-ID: Hi, You can also put a symlink in the directory with all the Emboss executables. I had to do this to get Emboss Explorer to work, even though both clustalw and primer3_core executables were in /usr/local/bin. I made a symlink in the Emboss-2.xxxx/bin directory and all was well. Andrew Bioinformatics Advanced Scientific Computing, Animal Genetics and Genomics, PIRVic Attwood 475 Mickleham Road, Attwood, 3049 ph +61 3 92174342 mob 0413 009 761 ---------------- There are 10 kinds of people...those who understand binary and those who don't. Sean.Maceachern at dpi.vic.gov.au Sent by: emboss-bounces at emboss.open-bio.org 19/08/05 09:01 AM To: anders.nister at lcb.uu.se cc: emboss at emboss.open-bio.org Subject: Re: [EMBOSS] emma/clustalw PATH problems I have had a simillar problem with eprimer3, a temporary fix will be to modify your path so that it can find the clustalw binary eg) export PATH=$PATH:/home/sm82/primer3_1.0.0/src anders.nister at lcb.uu.se Sent by: To: emboss at emboss.open-bio.org emboss-bounces at emboss.o cc: pen-bio.org Subject: [EMBOSS] emma/clustalw PATH problems 19/08/2005 12:46 AM I am trying to run emma, and for certain reasons i don't have clustalw in my PATH. Running emma produces this error: EMBOSS An error in ajsys.c at line 398: cannot find program 'clustalw' Looking through the manual for emma there is a mention of EMBOSS_CLUSTALW: "cannot find program 'clustalw'" - means that the ClustalW program has not been set up on your site or is not in your environment (i.e. is not on your path). The solutions are to (1) install clustalw in the path so that emma can find it with the command "clustalw", or (2) define a variable (an environment variable of in emboss.defaults or your .embossrc file) called EMBOSS_CLUSTALW containing the command (program name or full path) to run clustalw if you have it elsewhere on your system. So I'm supposed to be able to specify the full path to clustalw through EMBOSS_CLUSTALW.... Setting this variable to the full path of clustalw produces a similar error to the one before. EMBOSS An error in ajsys.c at line 398: cannot find program '/usr/local/bin/clustalw' Looking through the emma source code I can see that ajSystemEnv is used to execute clustalw, this function will always look through the PATH env variable for the executable it is trying to run, so specifying a full path does absolutely nothing to get around the problem. Is the documentation wrong or is this a bug ? Has anyone got a workaround ? Is there any emboss function for executing an external program directly, without it being present in PATH ? /Anders Nist?r _______________________________________________ EMBOSS mailing list EMBOSS at emboss.open-bio.org http://newportal.open-bio.org/mailman/listinfo/emboss _______________________________________________ EMBOSS mailing list EMBOSS at emboss.open-bio.org http://newportal.open-bio.org/mailman/listinfo/emboss From tjc at sanger.ac.uk Sat Aug 20 13:03:06 2005 From: tjc at sanger.ac.uk (Tim Carver) Date: Sat, 20 Aug 2005 18:03:06 +0100 (BST) Subject: [EMBOSS] emboss server In-Reply-To: <39102.129.111.174.49.1124381885.squirrel@biochem.uthscsa.edu> References: <39102.129.111.174.49.1124381885.squirrel@biochem.uthscsa.edu> Message-ID: Hi Jeremy Tomcat 5.5.* series will require Java 1.5. If you want to use java 1.4.2 you will need to use 5.0.28. So you will need to do a fresh install which means stopping tomcat and removing the tomcat, axis, and emboss installations. If you still have problems after re-installing check the tomcat logs ($TOMCAT/log/catalina.out) for error messages. Also ensure that you : -are running tomcat as the UID you define on installation -chown jembossctl to root and chmod u+s jembossctl. -ensure that the results directories are world read-writable. Hopefully this will help. Regards Tim Carver On Thu, 18 Aug 2005, Jeremy Mann wrote: > I still have not found the cure to my login problems with the EMBOSS > server. I've done the install several times now with and without > encryption, different kinds of authentication and nothing seems to work. > > With encryption selected I get: > No trusted certificate found > > I have done the encrypted install about a hundred times now and each time > it does make the certificate and I have edited the server.xml to reflect > the change. So I don't know what I'm missing here. > > Without encryption I don't get any errors, but the login prompt is always > popping up. I've tried all 6 types of authentication and none of them > work. > > I'm at my wits end and my head hurts from banging it on my desk ;) Could > somebody with a working Linux EMBOSS server contact me off or on list? > > Thanks a bunch! > > System: > Suse x86_64 9.1 > Java 1.4.2 > EMBOSS 3.0.0 > Latest Jemboss client > Tomcat 5.5.9 with compat library > Axis 1_2 > > > > -- > Jeremy Mann > jeremy at biochem.uthscsa.edu > > University of Texas Health Science Center > Bioinformatics Core Facility > http://www.bioinformatics.uthscsa.edu > Phone: (210) 567-2672 > > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss > The Wellcome Trust Sanger Institute Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK From smiddha at indiana.edu Sun Aug 21 01:12:21 2005 From: smiddha at indiana.edu (Sumit Middha) Date: Sun, 21 Aug 2005 00:12:21 -0500 Subject: [EMBOSS] emboss-explorer post installation In-Reply-To: References: Message-ID: <1124601141.43080d3568207@webmail.iu.edu> Hello Andrew, Thanks so much for your response. Probably I did not focus my question properly. Yes I did manage to install using the script, and specified the paths. However, I could not figure out, what my server should point to (I guess the index page in html). Also I am unsure of how the emboss installation gets linked to the explorer (I dont think I mentioned it anywhere during the installation of this emboss-explorer). And do you have or know of any comparisons, betwween emboss interfaces from w2h, pise and emboss-explorer ? Cheers, Sumit Quoting Andrew.Mather at dpi.vic.gov.au: > Hi Sumit, > > No, I don't really have any notes, because the installation is very > straightforward. > > The only thing I had to do was to edit the install script to point to my > perl binary, which is in /usr/local/bin, not /usr/bin. Once I did that > and ran the script, everything 'just worked', except for the clustal and > primer3_core issue. > > That was fixed by making a symbolic link in my Emboss bin directory to the > clustalw and primer3_core executables. Other than that, there was no > problem. > > When you run the script, it asks you where the various directories are and > installs things wherever you tell it. The only thing I'm not sure of is > if you need to have bioPerl installed beforehand. > > Because we have, it didn't ask about it, so I'm not sure. > > I did have quite a few problems with the previous version of > Emboss-explorer, which was called Emboss::GUI, however upgrading to the > current version removed all of those. > > Andrew > > > > Bioinformatics Advanced Scientific Computing, > Animal Genetics and Genomics, PIRVic Attwood > 475 Mickleham Road, Attwood, 3049 > ph +61 3 92174342 > mob 0413 009 761 > > > ---------------- > There are 10 kinds of people...those who understand binary and those who > don't. > > > > > > smiddha at indiana.edu > 20/08/05 02:20 PM > > > To: Andrew.Mather at dpi.vic.gov.au > cc: > Subject: Re: [EMBOSS] emma/clustalw PATH problems > > > > Hello Andrew, > Do you have notes on installation of Emboss-explorer? It would be great > help to > look at those for my installation. > > Thanks, > Sumit > > > Quoting Andrew.Mather at dpi.vic.gov.au: > > > Hi, > > > > You can also put a symlink in the directory with all the Emboss > > executables. > > > > I had to do this to get Emboss Explorer to work, even though both > clustalw > > and primer3_core executables were in /usr/local/bin. > > > > I made a symlink in the Emboss-2.xxxx/bin directory and all was well. > > > > Andrew > > > > > > > > Bioinformatics Advanced Scientific Computing, > > Animal Genetics and Genomics, PIRVic Attwood > > 475 Mickleham Road, Attwood, 3049 > > ph +61 3 92174342 > > mob 0413 009 761 > > > > > > ---------------- > > There are 10 kinds of people...those who understand binary and those who > > > don't. > > > > > > > > > > > > Sean.Maceachern at dpi.vic.gov.au > > Sent by: emboss-bounces at emboss.open-bio.org > > 19/08/05 09:01 AM > > > > > > To: anders.nister at lcb.uu.se > > cc: emboss at emboss.open-bio.org > > Subject: Re: [EMBOSS] emma/clustalw PATH problems > > > > > > > > I have had a simillar problem with eprimer3, a temporary fix will be to > > modify your path so that it can find the clustalw binary > > > > eg) > > > > export PATH=$PATH:/home/sm82/primer3_1.0.0/src > > > > > > > > > > > > > > anders.nister at lcb.uu.se > > Sent by: To: > > emboss at emboss.open-bio.org > > emboss-bounces at emboss.o cc: > > pen-bio.org Subject: [EMBOSS] > > emma/clustalw PATH problems > > > > > > 19/08/2005 12:46 AM > > > > > > > > > > > > > > I am trying to run emma, and for certain reasons i don't have clustalw > in > > my > > PATH. > > > > Running emma produces this error: > > > > EMBOSS An error in ajsys.c at line 398: > > cannot find program 'clustalw' > > > > > > Looking through the manual for emma there is a mention of > EMBOSS_CLUSTALW: > > > > "cannot find program 'clustalw'" - means that the ClustalW program > has > > not been set up on your site or is not in your environment (i.e. is > > not on your path). The solutions are to (1) install clustalw in the > > path so that emma can find it with the command "clustalw", or (2) > > define a variable (an environment variable of in emboss.defaults or > > your .embossrc file) called EMBOSS_CLUSTALW containing the command > > (program name or full path) to run clustalw if you have it elsewhere > > on your system. > > > > So I'm supposed to be able to specify the full path to clustalw through > > EMBOSS_CLUSTALW.... > > > > Setting this variable to the full path of clustalw produces a similar > > error > > to the one before. > > > > EMBOSS An error in ajsys.c at line 398: > > cannot find program '/usr/local/bin/clustalw' > > > > Looking through the emma source code I can see that ajSystemEnv is used > to > > execute clustalw, this function will always look through the PATH env > > variable for the executable it is trying to run, so specifying a full > path > > does absolutely nothing to get around the problem. > > > > Is the documentation wrong or is this a bug ? > > Has anyone got a workaround ? > > Is there any emboss function for executing an external program directly, > > without it being present in PATH ? > > > > /Anders Nist?r > > > > _______________________________________________ > > EMBOSS mailing list > > EMBOSS at emboss.open-bio.org > > http://newportal.open-bio.org/mailman/listinfo/emboss > > > > > > > > > > > > > > _______________________________________________ > > EMBOSS mailing list > > EMBOSS at emboss.open-bio.org > > http://newportal.open-bio.org/mailman/listinfo/emboss > > > > > > > > _______________________________________________ > > EMBOSS mailing list > > EMBOSS at emboss.open-bio.org > > http://newportal.open-bio.org/mailman/listinfo/emboss > > > > > From pmr at ebi.ac.uk Mon Aug 22 02:50:32 2005 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Mon, 22 Aug 2005 07:50:32 +0100 (BST) Subject: [EMBOSS] emboss-explorer post installation In-Reply-To: <1124601141.43080d3568207@webmail.iu.edu> References: <1124601141.43080d3568207@webmail.iu.edu> Message-ID: <1289.172.203.254.24.1124693432.squirrel@webmail.ebi.ac.uk> Dear Sumit, > And do you have or know of any comparisons, between emboss interfaces > from w2h, > pise and emboss-explorer ? I plan to send a survey to all the EMBOSS interfaces so that we can make a comparison on the EMBOSS website. This will take a little time to organise. So, does anyone already have a comparison? It would be helpful when I write the survey form. regards, Peter Rice From golharam at umdnj.edu Mon Aug 22 16:57:06 2005 From: golharam at umdnj.edu (Ryan Golhar) Date: Mon, 22 Aug 2005 16:57:06 -0400 Subject: [EMBOSS] Emma in EMBOSS Explorer Message-ID: <021201c5a75c$0e3a0380$2f01a8c0@GOLHARMOBILE1> In EMBOSS Explorer, using EMMA, one of the options under Slow align options is "Do you want to carry out slow or fast pairwise alignment? The options available is "Yes/No". Shouldn't that be slow/fast? -- Ryan Golhar - golharam at umdnj.edu The Informatics Institute of UMDNJ 973-972-5034 From rob.pollock at gmail.com Mon Aug 22 23:34:07 2005 From: rob.pollock at gmail.com (Rob Pollock) Date: Tue, 23 Aug 2005 15:34:07 +1200 Subject: [EMBOSS] Long Refseq accessions and dbifasta/seqret bug?? Message-ID: Hi, I download human.protein.faa from NCBI on a weekly basis and use dbifasta to build an emboss database. However, I have recently noticed that seqret has problems finding sequences with certain accessions, even though they are in the database. I suspect this is something to do with the new long RefSeq accessions and the way the index is built. Here is an example: (I call my RefSeq protein database 'genprot' for want of a better name) I am using EMBOSS 3.0.0 btw. (also Version 2.10.0 did the same thing) This fails: % seqret 'genprot:NP_001015.1' Reads and writes (returns) sequences Error: Unable to read sequence 'genprot:NP_001015.1' Died: seqret terminated: Bad value for '-sequence' and no prompt However this works: % seqret 'genprot:NP_001015' Reads and writes (returns) sequences Output sequence [np_001015.fasta]: % more np_001015.fasta >NP_001015.1 NP_001015.1 ribosomal protein S21 [Homo sapiens] MQNDAGEFVDLYVPRKCSASNRIIGAKDHASIQMNVAEVDKVTGRFNGQFKTYAICGAIR RMGESDDSILRLAKADGIVSKNF If I search human.protein.faa for strings that match NP_0010150 get a whole list: >gi|62632744|ref|NP_001015050.1| hypothetical protein LOC200810 [Homo sapiens] >gi|62821803|ref|NP_001015884.1| RPB11b2alpha protein [Homo sapiens] >gi|62865862|ref|NP_001015508.1| purine-rich element binding protein G isoform B [Homo sapiens] >gi|62865641|ref|NP_001015879.1| aurora kinaseatching NP_001015 I get a whole list: ... etc Again, using the full accession for any one of these fails: % seqret 'genprot:NP_001015071.1' Reads and writes (returns) sequences Error: Unable to read sequence 'genprot:NP_001015071.1' Died: seqret terminated: Bad value for '-sequence' and no prompt But, again, the truncated accession works: % seqret 'genprot:NP_001015071' Reads and writes (returns) sequences Output sequence [np_001015071.fasta]: Other sequences searched by full accession work fine (as long as they're _in_ the database!) % seqret 'genprot:NP_000544.1' Reads and writes (returns) sequences Output sequence [np_000544.fasta]: I think the long accessions are calling dbifasta/seqret to spit the dummy somehow. Note:This is how I format my database % dbifasta -dbname genprot -idformat ncbi -directory ~/genprot -filenames \*.faa -auto Maybe there is a workaround at this point?? Any suggestions?? [I have a file that includes sequences I need that aren't found in the current release of Refseq which is diff.faa, hence the -filenames \*.faa bit.] Thanks in advance Rob Pollock. From fernan at iib.unsam.edu.ar Tue Aug 23 08:56:13 2005 From: fernan at iib.unsam.edu.ar (Fernan Aguero) Date: Tue, 23 Aug 2005 09:56:13 -0300 Subject: [EMBOSS] Emma in EMBOSS Explorer In-Reply-To: <021201c5a75c$0e3a0380$2f01a8c0@GOLHARMOBILE1> References: <021201c5a75c$0e3a0380$2f01a8c0@GOLHARMOBILE1> Message-ID: <20050823125613.GJ15503@iib.unsam.edu.ar> +----[ Ryan Golhar (22.Aug.2005 18:17): | | In EMBOSS Explorer, using EMMA, one of the options under Slow align | options is "Do you want to carry out slow or fast pairwise alignment? | The options available is "Yes/No". Shouldn't that be slow/fast? | +----] In my particular view or reading of the meaning of the question I would say that if the question was "What kind (or speed) of pairwise alignment do you want?" then the options could be "Slow/Fast". But the question is just asking you to say Yes or No to whether you want something (a slow or fast alignment) or not. Anyway, EMMA is just a wrapper around clustalw. And that option comes from good ol' clustalw. So if you want it changed, I guess you have to bug the original authors ... But in the end (and apologies in advance since I know this is foreign to the EMBOSS culture/tradition), it doesn't really matter what colour we paint the bikeshed: http://www.freebsd.org/doc/en_US.ISO8859-1/books/faq/misc.html#BIKESHED-PAINTING Fernan From rob.pollock at gmail.com Wed Aug 24 01:22:47 2005 From: rob.pollock at gmail.com (Rob Pollock) Date: Wed, 24 Aug 2005 17:22:47 +1200 Subject: [EMBOSS] Long Refseq accessions and dbifasta/seqret bug?? SOLVED.. workaround In-Reply-To: References: Message-ID: Ok, well if you use dbxfasta and define a "resource" with sufficiently long (id and acc) fields, it works. % tfm dbxfasta for what I mean by resource On 8/23/05, Rob Pollock wrote: > Hi, > > I download human.protein.faa from NCBI on a weekly basis and use dbifasta to > build an emboss database. However, I have recently noticed that > seqret has problems > finding sequences with certain accessions, even though they are in the database. > > I suspect this is something to do with the new long RefSeq accessions > and the way > the index is built. Here is an example: (I call my RefSeq protein > database 'genprot' for > want of a better name) > > I am using EMBOSS 3.0.0 btw. (also Version 2.10.0 did the same thing) > > This fails: > > % seqret 'genprot:NP_001015.1' > Reads and writes (returns) sequences > Error: Unable to read sequence 'genprot:NP_001015.1' > Died: seqret terminated: Bad value for '-sequence' and no prompt > > However this works: > % seqret 'genprot:NP_001015' > Reads and writes (returns) sequences > Output sequence [np_001015.fasta]: > > % more np_001015.fasta > >NP_001015.1 NP_001015.1 ribosomal protein S21 [Homo sapiens] > MQNDAGEFVDLYVPRKCSASNRIIGAKDHASIQMNVAEVDKVTGRFNGQFKTYAICGAIR > RMGESDDSILRLAKADGIVSKNF > > If I search human.protein.faa for strings that match NP_0010150 get a > whole list: > > >gi|62632744|ref|NP_001015050.1| hypothetical protein LOC200810 [Homo sapiens] > >gi|62821803|ref|NP_001015884.1| RPB11b2alpha protein [Homo sapiens] > >gi|62865862|ref|NP_001015508.1| purine-rich element binding protein G > isoform B [Homo sapiens] > >gi|62865641|ref|NP_001015879.1| aurora kinaseatching NP_001015 I get > a whole list: > ... etc > > Again, using the full accession for any one of these fails: > > % seqret 'genprot:NP_001015071.1' > Reads and writes (returns) sequences > Error: Unable to read sequence 'genprot:NP_001015071.1' > Died: seqret terminated: Bad value for '-sequence' and no prompt > > But, again, the truncated accession works: > % seqret 'genprot:NP_001015071' > Reads and writes (returns) sequences > Output sequence [np_001015071.fasta]: > > Other sequences searched by full accession work fine (as long as > they're _in_ the > database!) > > % seqret 'genprot:NP_000544.1' > Reads and writes (returns) sequences > Output sequence [np_000544.fasta]: > > I think the long accessions are calling dbifasta/seqret to spit the > dummy somehow. > > Note:This is how I format my database > > % dbifasta -dbname genprot -idformat ncbi -directory ~/genprot > -filenames \*.faa -auto > > Maybe there is a workaround at this point?? Any suggestions?? > > [I have a file that includes sequences I need that aren't found in the current > release of Refseq which is diff.faa, hence the -filenames \*.faa bit.] > > Thanks in advance > Rob Pollock. > From dalloliogm at gmail.com Wed Aug 24 15:21:08 2005 From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio) Date: Wed, 24 Aug 2005 21:21:08 +0200 Subject: [EMBOSS] embossrc - configure database NPRD and AEdb Message-ID: <5aa3b3570508241221142887a8@mail.gmail.com> Hi all, I'm trying to configure this two databases in my .embossrc - emboss_default , but I didn't managed to get it works: http://srs6.bionet.nsc.ru/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+3Xn_71Qks76+-lib+NUCLEOSOME http://www.ebi.ac.uk/asd-srv/AEdb-query.cgi?method=MAIN&visit=first For the first one, I've tried this: DB NPRD [ method: srswww format: embl # url: " http://srs6.bionet.nsc.ru/srs6bin/cgi-bin/wgetz?-id+1YUkq1Qk6fN+-e+[NUCLEOSOME:'%s'] " # url: " http://srs6.bionet.nsc.ru/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+3Xn_71QkMvb+-lib+NUCLEOSOME " # url: " http://srs6.bionet.nsc.ru/srs6bin/cgi-bin/wgetz?-id+-e+[NUCLEOSOME:'%s']" url: "http://srs6.bionet.nsc.ru/srs6bin/cgi-bin/wgetz" type: N dbalias: NUCLEOSOME app: getz fields: "AC SQ" ] But what's is wrong? How can I understand what is the 'correct' url to choose, and how can I determine the right 'method' and 'format'? I've seen that in the main page of this database, there are description about the syntax and the and the structure in SRS. For example, can I use the informations described here: http://srs6.bionet.nsc.ru/srs6bin/cgi-bin/wgetz?-page+icarusFile+-id+3Xn_71Qks76+-l+NUCLEOSOME+-ifile+i? Thank you for any reply. Giovanni -- ----------------------------------------------------------- Visit my website! http://dalloliogm.altervista.org From ulrike.kaule at gmx.de Wed Aug 24 16:22:11 2005 From: ulrike.kaule at gmx.de (Ulrike Kaule) Date: Wed, 24 Aug 2005 22:22:11 +0200 Subject: [EMBOSS] output of program "digest" as input for program "pepstats" ? Message-ID: <430CD6F3.30306@gmx.de> Hello, I'm a new user to emboss. Within a Taverna-Workflow I want to digest a protein-sequence first with the emboss-program "digest" and to use the output of "digest" - the seqtable with the fragments - as an input for further sequence-analysis programs. So the resulting fragments should be analysed by pepstats or iep. But I have problems with the connection of these programs, because the output of "digest" is not accepted by the other programs as input. I thougth to solve this problem with using "seqret" between "digest" and "pepstats", but this doesn't work. Is there any solution to extract the protein-fragments produced by "digest" and to use them as input for other programs? Thank you in advance Ulrike From s_y_jeong at yahoo.com Wed Aug 24 20:24:56 2005 From: s_y_jeong at yahoo.com (Seong-Yun Jeong) Date: Wed, 24 Aug 2005 17:24:56 -0700 (PDT) Subject: [EMBOSS] Please remove my address Message-ID: <20050825002456.66798.qmail@web34015.mail.mud.yahoo.com> I don't want to get these mails. Please remove my address from the list. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From gbottu at ben.vub.ac.be Thu Aug 25 08:18:43 2005 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Thu, 25 Aug 2005 14:18:43 +0200 Subject: [EMBOSS] output of program "digest" as input for program "pepstats" ? In-Reply-To: <430CD6F3.30306@gmx.de> References: <430CD6F3.30306@gmx.de> Message-ID: <20050825121843.GA5549@bigben.ulb.ac.be> Dear Ulrike, You can ask digest for a "Report Format" of type "List File", which you can give as input to pepstats or iep (the peptides will be analyzed as individual sequences and the results given the one aftert the other, they are not merged). I have no experience with Taverna and hence cannot tell you exactly how to. I know that at the command line you would have to : digest mysequence -rformat=listfile -outfile=myreport iep list::myreport Regards, Guy Bottu, Belgian EMBnet Node From lukem at gene.pbi.nrc.ca Fri Aug 26 15:16:40 2005 From: lukem at gene.pbi.nrc.ca (Luke McCarthy) Date: Fri, 26 Aug 2005 13:16:40 -0600 Subject: [EMBOSS] emboss-explorer post installation In-Reply-To: <1124601141.43080d3568207@webmail.iu.edu> References: <1124601141.43080d3568207@webmail.iu.edu> Message-ID: <1125083799.6666.12.camel@incognito.invalid> On Sat, 2005-08-20 at 23:12, Sumit Middha wrote: > Hello Andrew, > Thanks so much for your response. Probably I did not focus my question properly. > Yes I did manage to install using the script, and specified the paths. > > However, I could not figure out, what my server should point to (I guess the > index page in html). At the end of the install script, there is a message containing some important information. One such piece of information is the URL to access the EMBOSS explorer interface. It says something like "Visit URL_TO_EMBOSS_EXPLORER to test it out." That's the URL you should use. The url you should use is the url to the CGI script (usually something like http://hostname/cgi-bin/emboss) > Also I am unsure of how the emboss installation gets linked > to the explorer (I dont think I mentioned it anywhere during the > installation of this emboss-explorer). I'm afraid I don't understand the question. The questions you answer during the install script provide all of the information EMBOSS explorer needs to find the EMBOSS installation. If you need to change this information at a later date, you can either re-run the install script, or edit the configuration module (the location of which is provided in the message at the end of the install script...) Cheers, Luke From smiddha at indiana.edu Mon Aug 29 17:30:15 2005 From: smiddha at indiana.edu (Sumit Middha) Date: Mon, 29 Aug 2005 16:30:15 -0500 Subject: [EMBOSS] emboss-explorer in non-default directory In-Reply-To: <1125083799.6666.12.camel@incognito.invalid> References: <1124601141.43080d3568207@webmail.iu.edu> <1125083799.6666.12.camel@incognito.invalid> Message-ID: <1125351015.43137e67ebdc2@webmail.iu.edu> Thanks Luke. Yes I figured that out. However, I get an error in the menu frame, when I open the emboss-explorer. Died: Qualifier '-showembassy' not found, referer: http://bioportal/cgi-bin/emboss/menu [Mon Aug 29 16:22:11 2005] [error] [client 156.56.96.41] , referer: http://bioportal/cgi-bin/emboss/menu [Mon Aug 29 16:22:11 2005] [error] [client 156.56.96.41] Can't use an undefined value as an ARRAY reference at /bioportal/web/tools/emboss-explorer/lib/EMBOSS/GUI/XHTML.pm line 317., referer: http://bioportal/cgi-bin/emboss/menu I am trying to fix this by making changes, but your help will be valuable. Quoting Luke McCarthy : > On Sat, 2005-08-20 at 23:12, Sumit Middha wrote: > > Hello Andrew, > > Thanks so much for your response. Probably I did not focus my question > properly. > > Yes I did manage to install using the script, and specified the paths. > > > > However, I could not figure out, what my server should point to (I > guess the > > index page in html). > > At the end of the install script, there is a message containing some > important information. One such piece of information is the URL to > access the EMBOSS explorer interface. It says something like "Visit > URL_TO_EMBOSS_EXPLORER to test it out." That's the URL you should use. > > The url you should use is the url to the CGI script (usually something > like http://hostname/cgi-bin/emboss) > > > Also I am unsure of how the emboss installation gets linked > > to the explorer (I dont think I mentioned it anywhere during the > > installation of this emboss-explorer). > > I'm afraid I don't understand the question. The questions you answer > during the install script provide all of the information EMBOSS explorer > needs to find the EMBOSS installation. If you need to change this > information at a later date, you can either re-run the install script, > or edit the configuration module (the location of which is provided in > the message at the end of the install script...) > > Cheers, > > Luke > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss > From golharam at umdnj.edu Tue Aug 30 00:20:37 2005 From: golharam at umdnj.edu (Ryan Golhar) Date: Tue, 30 Aug 2005 00:20:37 -0400 Subject: [EMBOSS] NCBI Blast in emboss-explorer Message-ID: <005501c5ad1a$2e1b6770$d33d140a@GOLHARMOBILE1> Has anyone tried incorporating NCBI Blast into the emboss-explorer UI? I haven't read the documentation yet on how to incorporate other applications into EMBOSS, as I was hoping someone else has already done this with BLAST :) Ryan From lukem at gene.pbi.nrc.ca Tue Aug 30 01:28:37 2005 From: lukem at gene.pbi.nrc.ca (Luke McCarthy) Date: Mon, 29 Aug 2005 23:28:37 -0600 Subject: [EMBOSS] NCBI Blast in emboss-explorer In-Reply-To: <005501c5ad1a$2e1b6770$d33d140a@GOLHARMOBILE1> References: <005501c5ad1a$2e1b6770$d33d140a@GOLHARMOBILE1> Message-ID: <1125379717.6049.12.camel@drmemory.private.virtuouspagans.org> On Mon, 2005-08-29 at 22:20, Ryan Golhar wrote: > Has anyone tried incorporating NCBI Blast into the emboss-explorer UI? > > I haven't read the documentation yet on how to incorporate other > applications into EMBOSS, as I was hoping someone else has already done > this with BLAST :) I don't know precisely what else is required to create an EMBOSS wrapper (a la emma) around an external program, but if your only concern is EMBOSS explorer, all you have to do is mock up an ACD file with the same name as the executable (in the same location as the other EMBOSS ACD files, usually /usr/local/share/EMBOSS/acd/ or something similar) and make sure the executable is in the EMBOSS explorer PATH (set in the configuration module, but by default it's the location of the EMBOSS binaries...) In the ACD file, the name of each parameter has to be the command line switch. For example: datafile: i [ required: "y" ] outfile: o [ required: "y" ] For best results, you'd have to put the options in appropriate sections, etc. The only tricky part I can see is that you'd have to hardcode your available BLAST databases in the ACD file. It's entirely possible that someone has already done this, or has written an actual EMBOSS wrapper for BLAST. If there is no such response forthcoming, I'll whip up a blastall.acd later this week and put it up on the EMBOSS explorer website. It would be a good way to showcase the flexibility of the interface and the ACD language itself. Cheers, Luke From ajb at ebi.ac.uk Tue Aug 30 03:28:55 2005 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Tue, 30 Aug 2005 08:28:55 +0100 (BST) Subject: [EMBOSS] NCBI Blast in emboss-explorer In-Reply-To: <1125379717.6049.12.camel@drmemory.private.virtuouspagans.org> References: <005501c5ad1a$2e1b6770$d33d140a@GOLHARMOBILE1> <1125379717.6049.12.camel@drmemory.private.virtuouspagans.org> Message-ID: <37186.172.31.70.99.1125386935.squirrel@webmail.ebi.ac.uk> Wrapping BLAST is on our things to do list for the medium term. I believe at least two sites have attempted this in the past. At the low level this is best done by splitting blastall into separate applications as it fits better with exposing them as web/GRID services. The blastall functionality can then be implemented as a GUI layer. As for the short term, we'll be watching with interest! Alan From gbottu at ben.vub.ac.be Tue Aug 30 06:17:57 2005 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Tue, 30 Aug 2005 12:17:57 +0200 Subject: [EMBOSS] NCBI BLAST under EMBOSS Message-ID: <20050830101757.GA10712@bigben.ulb.ac.be> Dear Ryan, dear all, You can download from http://www.wemboss.org/ wrappers4EMBOSS, which allows to access BLAST (as well as some other software) from under EMBOSS (as the standard distribution of EMBOSS already does for CLUSTAL and Primer3). Note by the way that an article about it appeared in EMBnet.news 11(1) (see http://www.embnet.org/download/embnetnews/). Some further remarks : - Just putting the blastall program in the EMBOSS .../bin directory and writing a blastall.acd file will not work well (only fastA format query sequence accepted, need to write absolute path to databanks in ACD file since the Web interface has no BLASTDB shell environment variable, etc.). Better is to write an EMBOSS "wrapper" program that starts by reading the ACD file and does whatever else is needed. Our "wrapper" can, among other things, generate on-the-fly from a List of sequences a databank to be searched. - Our "wrapper" works well in a terminal and under wEMBOSS. Since the ACD syntax is quite complex it does not run well under all GUI's. I know that the old EMBOSS-GUI of Luke did not manage well the hide/unhide of the parameters. I do not know how EMBOSS Explorer works ; I would like to hear about it as soon as somebody tested. To make BLAST work under all GUI's it might, as proposed, be needed to make separate programs for blastn, blastp, etc. - The databanks are indeed a problem. An EMBOSS library module that can find the databanks (as exists in GCG) would be nice. In the mean time, our wrappers need the databank names in the ACD files. As you will see if you try, wrappers4EMBOSS asks for the names of the databanks when you install it. A problem is that whenever you change the collection of databanks on your site you need to do the installation again or edit manually the ACD files. Hope this helps, Guy Bottu, Belgian EMBnet Node From David.Bauer at SCHERING.DE Mon Aug 1 06:36:46 2005 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Mon, 1 Aug 2005 08:36:46 +0200 Subject: [EMBOSS] Antwort: EMBOSS GUI problems In-Reply-To: Message-ID: Hi, I have installed the GUI last week and I can't reproduce this problem. water and needle with sequence pasted and uploaded from file run OK. Perl is 5.8.5 and Apache 1.3.26 on FreeBSD 4.9. David. emboss-bounces at emboss.open-bio.org schrieb am 30.07.2005 13:30:47: > Hi Luke and EMBOSS list > > I've installed the EMBOSS GUI and for the most part, it's working pretty > well. > > However for some apps (mainly seems to be alignment type ones like water, > needle, emma, but that may just be because I've tried more of them than > any others), it always fails > > Error: Unable to read sequence '' > Died: water terminated: Bad value for '-asequence' with -auto > defined > water exited with status 1... > > or in the /var/www/html/EMBOSS/runs/ error log, > > Error: Unable to read sequence '' > Died: water terminated: Bad value for '-asequence' with -auto defined > water exited with status 1... > > It doesn't seem to matter if it's sequence data pasted in, or uploaded > from a file. > > Some apps work fine, so I'm guessing it's not a fundamental problem like > permissions on a temp directory or something. > > Are you able to point me at where to start lookng ? > > Thanks, > Andrew > > > Animal Genetics and Genomics, PIRVic Attwood > 475 Mickleham Road, Attwood, 3049 > ph +61 3 92174342 > mob 0413 009 761 > > > ---------------- > There are 10 kinds of people...those who understand binary and those who > don't. > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss From pmr at ebi.ac.uk Mon Aug 1 09:05:00 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 01 Aug 2005 10:05:00 +0100 Subject: [EMBOSS] EMBOSS GUI problems In-Reply-To: References: Message-ID: <42EDE5BC.3070400@ebi.ac.uk> Andrew.Mather at dpi.vic.gov.au wrote: > Error: Unable to read sequence '' > Died: water terminated: Bad value for '-asequence' with -auto defined > water exited with status 1... This looks like what I would expect if there is no value for -asequence on the command line generated by EMBOSS::GUI. Luke ... over to you. Peter From Andrew.Mather at dpi.vic.gov.au Mon Aug 1 10:16:40 2005 From: Andrew.Mather at dpi.vic.gov.au (Andrew.Mather at dpi.vic.gov.au) Date: Mon, 1 Aug 2005 20:16:40 +1000 Subject: [EMBOSS] EMBOSS GUI problems Message-ID: Hi Peter, Yeah, that's what I figured too, but what's confused me is that it works for some apps, but not others. I guess I've assumed that something like getting the input sequence would be common to all apps but if it's not, that could explain some things. Andrew Animal Genetics and Genomics, PIRVic Attwood 475 Mickleham Road, Attwood, 3049 ph +61 3 92174342 mob 0413 009 761 ---------------- There are 10 kinds of people...those who understand binary and those who don't. pmr at ebi.ac.uk 01/08/05 07:05 PM To: Andrew.Mather at dpi.vic.gov.au cc: mcarthy at cs.usask.ca, emboss at emboss.open-bio.org Subject: Re: [EMBOSS] EMBOSS GUI problems Andrew.Mather at dpi.vic.gov.au wrote: > Error: Unable to read sequence '' > Died: water terminated: Bad value for '-asequence' with -auto defined > water exited with status 1... This looks like what I would expect if there is no value for -asequence on the command line generated by EMBOSS::GUI. Luke ... over to you. Peter From pmr at ebi.ac.uk Mon Aug 1 10:40:36 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 01 Aug 2005 11:40:36 +0100 Subject: [EMBOSS] EMBOSS GUI problems In-Reply-To: References: Message-ID: <42EDFC24.2010406@ebi.ac.uk> Andrew.Mather at dpi.vic.gov.au wrote: > Hi Peter, > > Yeah, that's what I figured too, but what's confused me is that it works > for some apps, but not others. > > I guess I've assumed that something like getting the input sequence would > be common to all apps but if it's not, that could explain some things. There are some dependiencies in the inputs for water and needle (both sequences must be protein or DNA) so they may have different processing. But emma has only one sequence input so that does not seem to be the common factor. Luke's address in your mail didn't work for me. I've copied this to another address for him (lukem at gene.pbi.nrc.ca). Peter > pmr at ebi.ac.uk > 01/08/05 07:05 PM > > > To: Andrew.Mather at dpi.vic.gov.au > cc: mcarthy at cs.usask.ca, emboss at emboss.open-bio.org > Subject: Re: [EMBOSS] EMBOSS GUI problems > > > Andrew.Mather at dpi.vic.gov.au wrote: > > >>Error: Unable to read sequence '' >>Died: water terminated: Bad value for '-asequence' with -auto defined >>water exited with status 1... > > > This looks like what I would expect if there is no value for -asequence on > the > command line generated by EMBOSS::GUI. > > Luke ... over to you. > > Peter > > > > From pmr at ebi.ac.uk Mon Aug 1 15:49:26 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 01 Aug 2005 16:49:26 +0100 Subject: [EMBOSS] Using seqret to fetch from .nal index databases In-Reply-To: <5C75DDA3-04A4-4A58-B925-31F9F017D8C4@uidaho.edu> References: <5C75DDA3-04A4-4A58-B925-31F9F017D8C4@uidaho.edu> Message-ID: <42EE4486.50302@ebi.ac.uk> Audra Johnson wrote: > Apologies for the length, but I want to be thorough. I'm doing blast > searches and then trying to fetch the sequences from the our genembl > database using seqret. For example: > > blastall -p tblastn /gcgdata_10.3/gcgblast/genembl -i > dp00061_disordered_115_168.fasta > I've tried using a seqret just for the database name I'm giving > blastall, and specifically saying the genembl.nal file: > > $ seqret > Reads and writes (returns) sequences > Input sequence(s): /gcgdata_10.3/gcgblast/genembl.nal:HUMRPA70KD > Error: Unable to read sequence '/gcgdata_10.3/gcgblast/ > genembl.nal:HUMRPA70KD' EMBOSS cannot read blast database files directly. EMBOSS can read the old format index files produced by formatdb, but not the latest ones - we have not yet decoded the index format. If you still have the FASTA format file /gcgdata_10.3/gcgblast/genembl then you can index this file with dbifasta (or dbxfasta using the new beta version indexing) and define it as a database for seqret - of use it in seqret the way you aer trying to use the .nal file (but this will be slow as it has to read the file until it fins the entry). If you have the same database in GCG format you can index it with dbigcg (or dbxgcg). If you use dbigcg or dbxgcg you may be able to use the GB_PR "gcg" database names in EMBOSS, by reusing the dbigcg indices with different files selected or excluded. Let me know if you would like more hints on how to do any of these. regards, Peter Rice From lukem at gene.pbi.nrc.ca Tue Aug 2 19:23:39 2005 From: lukem at gene.pbi.nrc.ca (Luke McCarthy) Date: Tue, 02 Aug 2005 13:23:39 -0600 Subject: [EMBOSS] EMBOSS GUI problems In-Reply-To: References: Message-ID: <1123010619.11724.15.camel@incognito.invalid> On Sat, 2005-07-30 at 04:40, Andrew.Mather at dpi.vic.gov.au wrote: > However for some apps (mainly seems to be alignment type ones like water, > needle, emma, but that may just be because I've tried more of them than > any others), it always fails > > Error: Unable to read sequence '' > Died: water terminated: Bad value for '-asequence' with -auto > defined > water exited with status 1... Do all of the applications that are failing require sequence input? Do all applications that require sequence input fail? What version of EMBOSS are you using (you can run embossversion from the GUI to get the number...) This is a really strange problem because sequence input isn't treated any differently from other input. Can you run applications that require other input files that aren't sequences? abiview, for example? What is happening here is that there is no value being passed for the 'asequence' parameter. When the input form is generated, it should be generating a field for the 'asequence' parameter. So, assuming you've filled in that field before trying to submit the input form, this shouldn't happen. One thing that occurs to me is that the naming convention for sequence parameters changed at some point (they used to be called sequencea/sequenceb and are now called asequence/bsequence...) Is it possible that the GUI is finding older versions of the ACD files? From the error output, it's clear that the version of water being run is looking for a parameter called 'asequence', but if the GUI read an old version of the ACD file when it generated the input page and thinks the parameter is called 'sequencea', maybe that's the problem? You can look in the EMBOSS::GUI::Conf module (the install script will have told you where it was installed to) and check the values of $EMBOSS_PREFIX, $EMBOSS_BIN and $EMBOSS_ACDROOT to make sure it's using the binaries and ACD files from the same EMBOSS version. This is actually very unlikely, as the GUI looks at the ACD file when it's building the command line, too. So it would have to find one ACD file when it was building the input form, and a different ACD file when it tried to run the application. > Some apps work fine, so I'm guessing it's not a fundamental problem like > permissions on a temp directory or something. No, if the temporary directory wasn't writable, all applications would fail. If your EMBOSS server is publicly accessible, email me (at lukem at gene.pbi.nrc.ca) with the URL and I'll poke around and try to figure out what's going on. Cheers, Luke From shrish at ccmb.res.in Wed Aug 3 09:35:14 2005 From: shrish at ccmb.res.in (Shrish Tiwari) Date: Wed, 3 Aug 2005 16:05:14 +0630 Subject: [EMBOSS] (no subject) Message-ID: Hi! I was installing the latest version of EMBOSS 3.0 and noticed during the make command the following: creating yank Making all in test No suffix list Making all in data No suffix list ... What does this mean? Shrish ______________________________________________________________________ Dr. Shrish Tiwari, Scientist BIC, Centre for Cellular and Molecular Biology Uppal Road, Hyderabad - 500 007 Phone: 91-40-7192776 (work), 91-40-7156603 (home) email: shrish at ccmb.res.in ______________________________________________________________________ From ajb at ebi.ac.uk Wed Aug 3 10:54:36 2005 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Wed, 3 Aug 2005 11:54:36 +0100 (BST) Subject: [EMBOSS] suffix list message In-Reply-To: References: Message-ID: <32918.172.31.70.166.1123066476.squirrel@webmail.ebi.ac.uk> The suffix list message will happen with some versions/installations of 'make' and can be safely ignored. It generally means that no files with the extension .c, .cc, .C, .p, .f, .F, .r, .y, .l, .s, .S, et cetera can be found in a particular directory. So, the message will usually be given in directories with no source code (etc). HTH Alan Bleasby EBI From george.magklaras at biotek.uio.no Thu Aug 11 16:29:56 2005 From: george.magklaras at biotek.uio.no (George Magklaras) Date: Thu, 11 Aug 2005 18:29:56 +0200 Subject: [EMBOSS] EMBASSY on EMBOSS 3.0.0 on RHEL WS 4 Message-ID: <42FB7D04.3020005@biotek.uio.no> Hi, Note: I realize this is EMBASSY, but I thought about dropping a note to you folks, as I am sure it is very likely you have seen this. After compiling separately zlib (1.2.3), libpng (1.2.8) and gd (2.0.33), I did a flawless EMBOSS 3.0.0 installation, and most embassy packages also compile properly. However, make on the PHYLIP-3.6b package quits with the following error message in response to the configure and make: ./configure --prefix=/mn/biotin/site --with-pngdriver=/mn/biotin/site/lib then make and I get the error: . . . gcc -O2 -o fconsense consense.o cons.o phylip.o -L/mn/biotin/site/lib/lib -L/mn/biotin/site/lib /mn/biotin/site/lib/libnucleus.so /mn/biotin/site/lib/libajax.so /mn/biotin/site/lib/libplplot.so -L/usr/X11R6/lib /mn/biotin/site/lib/libgd.so -L/usr/lib -lXpm -lX11 /usr/lib/libjpeg.so -lfontconfig /usr/lib/libfreetype.so -lpng12 -lpng -lz -lm /mn/biotin/site/lib/libz.a(compress.o)(.text+0xa0): In function `compress': : multiple definition of `compress' cons.o(.text+0x4e0): first defined here /usr/bin/ld: Warning: size of symbol `compress' changed from 326 in cons.o to 163 in /mn/biotin/site/lib/libz.a(compress.o) As far as I can see, the config log indicates that the cmd line got the options and the relevant libraries were found: checking if png driver is wanted... yes checking for inflateEnd in -lz... yes checking for png_destroy_read_struct in -lpng... yes checking for gdImageCreateFromPng in -lgd... yes PNG libraries found My compiler is: biotin.uio.no# gcc -v Reading specs from /usr/lib/gcc/i386-redhat-linux/3.4.3/specs Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-java-awt=gtk --host=i386-redhat-linux Thread model: posix gcc version 3.4.3 20050227 (Red Hat 3.4.3-22.1) Is this a library mix and match problem, or do I need another compiler...or...? Best Regards, GM -- -- George B. Magklaras Senior Computer Systems Engineer/UNIX Systems Administrator The Biotechnology Centre of Oslo, University of Oslo http://www.biotek.uio.no/ EMBnet Norway: http://www.biotek.uio.no/EMBNET/ Tel: +47-22840535 -- From ajb at ebi.ac.uk Thu Aug 11 17:34:17 2005 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Thu, 11 Aug 2005 18:34:17 +0100 (BST) Subject: [EMBOSS] EMBASSY on EMBOSS 3.0.0 on RHEL WS 4 In-Reply-To: <42FB7D04.3020005@biotek.uio.no> References: <42FB7D04.3020005@biotek.uio.no> Message-ID: <34006.81.96.71.66.1123781657.squirrel@webmail.ebi.ac.uk> That's the first report we've had of that problem. All compilers we've tried have let that error pass and correctly guessed the meaning of the code. Nevertheless it is an error so thanks for reporting it. I have just put a replacement file as ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIP-3.6b.tar.gz for anyone who has experienced the same compilation problem. HTH Alan Bleasby EBI From jeremy at biochem.uthscsa.edu Thu Aug 11 18:27:05 2005 From: jeremy at biochem.uthscsa.edu (Jeremy Mann) Date: Thu, 11 Aug 2005 13:27:05 -0500 (CDT) Subject: [EMBOSS] Difficulty with login Message-ID: <46012.129.111.174.49.1123784825.squirrel@biochem.uthscsa.edu> I'm trying to setup a jemboss server for a few researchers here and I have a problem I can't find an answer too. For some reason I can't login with a valid user account. When I run the client in debug mode, I get: javax.net.ssl.SSLHandshakeException: sun.security.validator.ValidatorException: No trusted certificate found I can't find this in the documentation. What exactly do I need to do to get this "trusted certificate"?? Thanks.. -- Jeremy Mann jeremy at biochem.uthscsa.edu University of Texas Health Science Center Bioinformatics Core Facility http://www.bioinformatics.uthscsa.edu Phone: (210) 567-2672 From tjc at sanger.ac.uk Fri Aug 12 07:58:55 2005 From: tjc at sanger.ac.uk (Tim Carver) Date: Fri, 12 Aug 2005 08:58:55 +0100 Subject: [EMBOSS] Difficulty with login In-Reply-To: <46012.129.111.174.49.1123784825.squirrel@biochem.uthscsa.edu> Message-ID: Hi Jeremy There are a number of reasons why it may complain about authentication. Here are the common ones: 1. the jembossctl script is not set to root and chmod'ed u+s 2. the results directory is not world read-writable 3. the tomcat server is not being run with the same UID that was given to the installation script However, from the look of the error you get it seems unlikely to be these. If you select SSL/Https for the protocol then the install script creates client & server certificates. These are used when connecting to the server to validate with the SSL handshake. You should first check your tomcat logs to see if the server is complaining about not finding this ($TOMCAT/logs/catalina.out). This should give some clues as to why you get that exception. Regards Tim Carver On 11/8/05 7:27 pm, "Jeremy Mann" wrote: > I'm trying to setup a jemboss server for a few researchers here and I have > a problem I can't find an answer too. For some reason I can't login with a > valid user account. When I run the client in debug mode, I get: > > javax.net.ssl.SSLHandshakeException: > sun.security.validator.ValidatorException: No trusted certificate found > > I can't find this in the documentation. What exactly do I need to do to > get this "trusted certificate"?? > > Thanks.. > > From benys at usp.br Wed Aug 17 13:01:16 2005 From: benys at usp.br (Beny Spira) Date: Wed, 17 Aug 2005 10:01:16 -0300 Subject: [EMBOSS] EMBOSS explorer In-Reply-To: <1121980112.5376.11.camel@incognito.invalid> References: <1121980112.5376.11.camel@incognito.invalid> Message-ID: <200508171001.17220.benys@usp.br> Hi Luke I would like to install EMBOSS explorer for the first time. I downloaded the source, but it says it needs some CPAN modules. I found those modules but do not know how to use them. How to install the whole package or is there any basic literature to read about it? Thank you in advance, Beny > Hi everybody, > > I'm pleased to finally announce a new release of the EMBOSS interface > formerly known as EMBOSS::GUI, now known as EMBOSS explorer. > > Development has moved to SourceForge.net and the new home page for the > interface is http://embossgui.sourceforge.net/ It's quite spartan at > the moment, but I'll be adding a FAQ as questions are frequent asked > (and answered...) > > You can download EMBOSS explorer at > http://prdownloads.sourceforge.net/embossgui/emboss-explorer-2.0.0.tar.gz?d >ownload > > The new release has been tested against EMBOSS-3.0.0, but not > thoroughly. Please report bugs using the bug tracker at > http://sourceforge.net/tracker/?atid=699414&group_id=124389&func=browse > (as a last resort, email them to mccarthy at users.sourceforge.net, but I'm > hoping that use of the bug tracker will help with duplicate reports and > other organizational issues...) > > Cheers, > > Luke > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Beny Spira Departamento de Microbiologia Instituto de Ci?ncias Biom?dicas Universidade de S?o Paulo Av. Prof. Lineu Prestes 1374 S?o Paulo-SP CEP:05508-900 Tel: 5511-3091-7347 FAX: 5511-3091-7354 E-mail: benys at usp.br %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From yuichiyoshi at gmail.com Wed Aug 17 17:09:59 2005 From: yuichiyoshi at gmail.com (Yoshida Yuichi) Date: Thu, 18 Aug 2005 02:09:59 +0900 Subject: [EMBOSS] emboss.defaut to access the enspep Message-ID: Hi, everyone, There is the following descriptions in the document of showdb command (/usr/share/EMBOSS/doc/programs/text/showdb.txt) > % showdb > Displays information on the currently available databases > > # Name Type ID Qry All Comment > # ==== ==== == === === ======= > enspep P OK OK OK ENSEMBL pep > enspepp P OK OK OK ENSEMBL pep predicted But I can't access the enspep (ENSEMBL pep) and enspepp (ENSEMBL pep predicted) by the showdb command. How should I describe the emboss.default (or .embossrc) to be able to access the enspep and enspepp. Would you please show me how to write the emboss.defaut (or .embossrc) in my case? ----- Yuichi Yoshida From jison at ebi.ac.uk Thu Aug 18 06:57:45 2005 From: jison at ebi.ac.uk (Jon Ison) Date: Thu, 18 Aug 2005 07:57:45 +0100 (BST) Subject: [EMBOSS] emboss.defaut to access the enspep In-Reply-To: References: Message-ID: <40155.172.31.8.12.1124348265.squirrel@webmail.ebi.ac.uk> Dear Yuichi enspep and enspepp are just examples used in the showdb documentation. You would need to create a database definition in your 'emboss.default' file (or '.embossrc' in your home directory). Instructions are here: http://emboss.sourceforge.net/docs/themes/Databases.html Get back in touch if you get stuck. J:) > Hi, everyone, > > There is the following descriptions in the document of showdb > command (/usr/share/EMBOSS/doc/programs/text/showdb.txt) > >> % showdb >> Displays information on the currently available databases >> >> # Name Type ID Qry All Comment >> # ==== ==== == === === ======= >> enspep P OK OK OK ENSEMBL pep >> enspepp P OK OK OK ENSEMBL pep predicted > > But I can't access the enspep (ENSEMBL pep) and enspepp > (ENSEMBL pep predicted) by the showdb command. > > How should I describe the emboss.default (or .embossrc) to > be able to access the enspep and enspepp. > > Would you please show me how to write the emboss.defaut > (or .embossrc) in my case? > > ----- > Yuichi Yoshida > > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss > From jison at ebi.ac.uk Thu Aug 18 07:01:33 2005 From: jison at ebi.ac.uk (Jon Ison) Date: Thu, 18 Aug 2005 08:01:33 +0100 (BST) Subject: [EMBOSS] Yoshida Yuishi ... Message-ID: <40158.172.31.8.12.1124348493.squirrel@webmail.ebi.ac.uk> emboss at emboss.open-bio.org From pmr at ebi.ac.uk Thu Aug 18 09:30:29 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 18 Aug 2005 10:30:29 +0100 Subject: [EMBOSS] emboss.defaut to access the enspep In-Reply-To: References: Message-ID: <43045535.8040505@ebi.ac.uk> Yoshida Yuichi wrote: > Hi, everyone, > > There is the following descriptions in the document of showdb > command (/usr/share/EMBOSS/doc/programs/text/showdb.txt) > > >>% showdb >>Displays information on the currently available databases >> >># Name Type ID Qry All Comment >># ==== ==== == === === ======= >>enspep P OK OK OK ENSEMBL pep >>enspepp P OK OK OK ENSEMBL pep predicted > > > But I can't access the enspep (ENSEMBL pep) and enspepp > (ENSEMBL pep predicted) by the showdb command. > > How should I describe the emboss.default (or .embossrc) to > be able to access the enspep and enspepp. The current showdb.txt file does not use enspep or enspepp as databases. A little history ... We generate the showdb.txt file from EMBOSS documentation on the website http://emboss.sourceforge.net/apps/showdb.html for each release. The usage example and the example output are in turn generated from our QA test suite. Your installation's showdb.txt file may be from an old release of EMBOSS, before we started to build the files from sourceforge. The older versions of showdb.txt used the databases installed at HGMP/RFCGR, where the EMBOSS developers were working. This institute has now closed and the development has moved to all be at EBI. The showdb.txt file was updated a year ago in release 2.10.0 when we started to move files from the HGMP website to sourceforge. If I recall correctly, HGMP's enspep and enspepp databases pointed to their SRS server, which has also closed. The ENSPEP database can be defined (for single entries only) using the Sanger Centre's SRS server: DB enspep [ type: "N" method: "SRSWWW" format: "fasta" url: "http://srs.sanger.ac.uk/srs7bin/cgi-bin/wgetz" dbalias: "ensemblpep" comment: "ensembl pep" ] To define is for multiple entries, use "methodquery" instead of "method" - this will allow you to use wildcard IDs. There is a list of publicly available SRS servers at http://downloads.lionbio.co.uk/publicsrs.html (liked to the EBI server's fron page. I can find nothing to match HGMP's "enspepp" database - unless it was simply a duplicate of the enspep database with a different access method. Sadly, the HGMP SRS server had more databases than any other server in the world. Some of them were not available anywhere else. HGMP may have also indexed enspep and enspepp in some other way (with dbifasta or dbiflat), using the ENSEMBL flatfiles from ftp.ensembl.org for example ftp://ftp.ensembl.org/pub/current_human/data/fasta/pep/ (for FASTA format files) or ftp://ftp.ensembl.org/pub/current_human/data/embl/pep/ for "embl" format files. There are separate files for some species that HGMP may have used for their two databases enspep and enspepp. We are working on ways to generate more information from showdb so that we can find out more about the database definitions (for sites that still exist!) in a future release. Hope that helps Peter Rice From anders.nister at lcb.uu.se Thu Aug 18 14:46:03 2005 From: anders.nister at lcb.uu.se (Anders =?ISO-8859-1?Q?Nist=E9r?=) Date: Thu, 18 Aug 2005 14:46:03 +0000 Subject: [EMBOSS] emma/clustalw PATH problems Message-ID: <20050818144603.E409E1E8@colibri.its.uu.se> I am trying to run emma, and for certain reasons i don't have clustalw in my PATH. Running emma produces this error: EMBOSS An error in ajsys.c at line 398: cannot find program 'clustalw' Looking through the manual for emma there is a mention of EMBOSS_CLUSTALW: "cannot find program 'clustalw'" - means that the ClustalW program has not been set up on your site or is not in your environment (i.e. is not on your path). The solutions are to (1) install clustalw in the path so that emma can find it with the command "clustalw", or (2) define a variable (an environment variable of in emboss.defaults or your .embossrc file) called EMBOSS_CLUSTALW containing the command (program name or full path) to run clustalw if you have it elsewhere on your system. So I'm supposed to be able to specify the full path to clustalw through EMBOSS_CLUSTALW.... Setting this variable to the full path of clustalw produces a similar error to the one before. EMBOSS An error in ajsys.c at line 398: cannot find program '/usr/local/bin/clustalw' Looking through the emma source code I can see that ajSystemEnv is used to execute clustalw, this function will always look through the PATH env variable for the executable it is trying to run, so specifying a full path does absolutely nothing to get around the problem. Is the documentation wrong or is this a bug ? Has anyone got a workaround ? Is there any emboss function for executing an external program directly, without it being present in PATH ? /Anders Nist?r From george.magklaras at biotek.uio.no Thu Aug 18 15:15:57 2005 From: george.magklaras at biotek.uio.no (George Magklaras) Date: Thu, 18 Aug 2005 17:15:57 +0200 Subject: [EMBOSS] emma/clustalw PATH problems In-Reply-To: <20050818144603.E409E1E8@colibri.its.uu.se> References: <20050818144603.E409E1E8@colibri.its.uu.se> Message-ID: <4304A62D.6020408@biotek.uio.no> How about placing the clustalw binary ( I assume that you have compiled this separately) into the same directory where you have the emboss binaries? If every other aspect of your EMBOSS install is OK then that should work? GM -- -- George B. Magklaras Senior Computer Systems Engineer/UNIX Systems Administrator The Biotechnology Centre of Oslo, University of Oslo http://www.biotek.uio.no/ EMBnet Norway: http://www.biotek.uio.no/EMBNET/ Anders Nist?r wrote: >I am trying to run emma, and for certain reasons i don't have clustalw in my >PATH. > >Running emma produces this error: > > EMBOSS An error in ajsys.c at line 398: >cannot find program 'clustalw' > > >Looking through the manual for emma there is a mention of EMBOSS_CLUSTALW: > > "cannot find program 'clustalw'" - means that the ClustalW program has > not been set up on your site or is not in your environment (i.e. is > not on your path). The solutions are to (1) install clustalw in the > path so that emma can find it with the command "clustalw", or (2) > define a variable (an environment variable of in emboss.defaults or > your .embossrc file) called EMBOSS_CLUSTALW containing the command > (program name or full path) to run clustalw if you have it elsewhere > on your system. > >So I'm supposed to be able to specify the full path to clustalw through >EMBOSS_CLUSTALW.... > >Setting this variable to the full path of clustalw produces a similar error >to the one before. > > EMBOSS An error in ajsys.c at line 398: >cannot find program '/usr/local/bin/clustalw' > >Looking through the emma source code I can see that ajSystemEnv is used to >execute clustalw, this function will always look through the PATH env >variable for the executable it is trying to run, so specifying a full path >does absolutely nothing to get around the problem. > >Is the documentation wrong or is this a bug ? >Has anyone got a workaround ? >Is there any emboss function for executing an external program directly, >without it being present in PATH ? > >/Anders Nist?r > >_______________________________________________ >EMBOSS mailing list >EMBOSS at emboss.open-bio.org >http://newportal.open-bio.org/mailman/listinfo/emboss > > From gbottu at ben.vub.ac.be Thu Aug 18 15:30:20 2005 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Thu, 18 Aug 2005 17:30:20 +0200 Subject: [EMBOSS] emma/clustalw PATH problems In-Reply-To: <20050818144603.E409E1E8@colibri.its.uu.se> References: <20050818144603.E409E1E8@colibri.its.uu.se> Message-ID: <20050818153020.GA15471@bigben.ulb.ac.be> On Thu, Aug 18, 2005 at 02:46:03PM +0000, Anders Nist?r wrote: > I am trying to run emma, and for certain reasons i don't have clustalw in my > PATH. > How about placing the clustalw binary ( I assume that you have compiled > this separately) into the same directory where you have the emboss > binaries? I think the best is to put in the directory with the EMBOSS binaries a logical link pointing to clustalw. Note by the way that you also need a logical link to primer3_core to make eprimer3 work. Guy Bottu, Belgian EMBnet Node From anders.nister at lcb.uu.se Thu Aug 18 16:13:12 2005 From: anders.nister at lcb.uu.se (Anders =?ISO-8859-1?Q?Nist=E9r?=) Date: Thu, 18 Aug 2005 16:13:12 +0000 Subject: [EMBOSS] emma/clustalw PATH problems In-Reply-To: <4304A62D.6020408@biotek.uio.no> Message-ID: <20050818161312.4CBA71E8@colibri.its.uu.se> Den 8/18/2005, skrev "George Magklaras" : >How about placing the clustalw binary ( I assume that you have compiled >this separately) into the same directory where you have the emboss >binaries? If every other aspect of your EMBOSS install is OK then that >should work? > >GM Unfortunately the binaries already are in the same directory, I am calling emma with the full path from a Cocoa application (PATH is not set)... /Anders Nist?r From jeremy at biochem.uthscsa.edu Thu Aug 18 16:18:05 2005 From: jeremy at biochem.uthscsa.edu (Jeremy Mann) Date: Thu, 18 Aug 2005 11:18:05 -0500 (CDT) Subject: [EMBOSS] emboss server Message-ID: <39102.129.111.174.49.1124381885.squirrel@biochem.uthscsa.edu> I still have not found the cure to my login problems with the EMBOSS server. I've done the install several times now with and without encryption, different kinds of authentication and nothing seems to work. With encryption selected I get: No trusted certificate found I have done the encrypted install about a hundred times now and each time it does make the certificate and I have edited the server.xml to reflect the change. So I don't know what I'm missing here. Without encryption I don't get any errors, but the login prompt is always popping up. I've tried all 6 types of authentication and none of them work. I'm at my wits end and my head hurts from banging it on my desk ;) Could somebody with a working Linux EMBOSS server contact me off or on list? Thanks a bunch! System: Suse x86_64 9.1 Java 1.4.2 EMBOSS 3.0.0 Latest Jemboss client Tomcat 5.5.9 with compat library Axis 1_2 -- Jeremy Mann jeremy at biochem.uthscsa.edu University of Texas Health Science Center Bioinformatics Core Facility http://www.bioinformatics.uthscsa.edu Phone: (210) 567-2672 From pmr at ebi.ac.uk Thu Aug 18 17:13:04 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 18 Aug 2005 18:13:04 +0100 Subject: [EMBOSS] emma/clustalw PATH problems In-Reply-To: <20050818144603.E409E1E8@colibri.its.uu.se> References: <20050818144603.E409E1E8@colibri.its.uu.se> Message-ID: <4304C1A0.8040206@ebi.ac.uk> Anders Nist?r wrote: > Looking through the manual for emma there is a mention of EMBOSS_CLUSTALW: > > "cannot find program 'clustalw'" - means that the ClustalW program has > not been set up on your site or is not in your environment (i.e. is > not on your path). The solutions are to (1) install clustalw in the > path so that emma can find it with the command "clustalw", or (2) > define a variable (an environment variable of in emboss.defaults or > your .embossrc file) called EMBOSS_CLUSTALW containing the command > (program name or full path) to run clustalw if you have it elsewhere > on your system. > > So I'm supposed to be able to specify the full path to clustalw through > EMBOSS_CLUSTALW.... > > Is the documentation wrong or is this a bug ? Ouch. It is a bug. The variable was originally set to allow older or newer versions of clustalw to be called. We have not tested programs that are not in the path. I am sure we can find a workaround for a fully specified path to the program. regards, Peter From andrespinzon at gmail.com Thu Aug 18 17:46:08 2005 From: andrespinzon at gmail.com (Andres Pinzon) Date: Thu, 18 Aug 2005 12:46:08 -0500 Subject: [EMBOSS] emboss server In-Reply-To: <39102.129.111.174.49.1124381885.squirrel@biochem.uthscsa.edu> References: <39102.129.111.174.49.1124381885.squirrel@biochem.uthscsa.edu> Message-ID: <8968fc7e05081810462e89b78c@mail.gmail.com> 2005/8/18, Jeremy Mann : > I'm at my wits end and my head hurts from banging it on my desk ;) Could > somebody with a working Linux EMBOSS server contact me off or on list? Hi, I really dont know what you mean with an "EMBOSS server", what I actually have is a GNU/Linux webserver on top of which emboss runs. We have several wEMBOSS/EMBOSSGUI users as well as command line EMBOSS users via SSH. If I can help u please ask me. ;-) -- --------- Andr?s Pinz?n [http://www.andrespinzon.com] Bioinformatics Center, Colombia EMBnet node Biotechnology Institute - National University of Colombia http://bioinf.ibun.unal.edu.co Tel +57 3165000 ext 16961 Fax +571 3165415 ---------- From dalloliogm at fastwebnet.it Thu Aug 18 19:07:04 2005 From: dalloliogm at fastwebnet.it (Dall'Olio Giovanni) Date: Thu, 18 Aug 2005 21:07:04 +0200 Subject: [EMBOSS] transfac site.dat ftp address Message-ID: <42F8C5A800003F7F@ms003msg.mail.fw> Hi all, Pleased to know you, I'm a student of bioinformatics from Barcelona. I was trying to use the 'tfscan' tool, but I can't find an ftp server to download the 'site.dat' file that is required for this tool. I've searched in Internet with google but I've only found this, that seems to be down: http://transfac.gbf.de/cgi-bin/download/download.pl Someone can help me in any way? I will appreciate it a lot. Thank you! --------------------------------------------- Dall'Olio Giovanni Marco, studente di Biotecnologie all'Universit? di Bologna. puoi trovarmi anche all'indirizzo dalloliogm at gmail.it p.s. visita il mio sito!! www.dalloliogm.tk (o http://dalloliogm.altervista.org) questo haiku e' dedicato a tutti coloro che ancora usano Windows: A file that big? It might be very useful. But now it is gone. -- David J. Liszewski Un file cos? grande? / Poteva esserti molto utile. / Ma adesso non c'? pi? http://digilander.libero.it/bunix/haiku.html From golharam at umdnj.edu Thu Aug 18 19:10:52 2005 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 18 Aug 2005 15:10:52 -0400 Subject: [EMBOSS] emma/clustalw PATH problems In-Reply-To: <4304C1A0.8040206@ebi.ac.uk> Message-ID: <00ea01c5a428$8da8bc60$2f01a8c0@GOLHARMOBILE1> I ran into the same problem. I simply moved clustalw into a directory in my path and everything works okay... -----Original Message----- From: emboss-bounces at emboss.open-bio.org [mailto:emboss-bounces at emboss.open-bio.org] On Behalf Of Peter Rice Sent: Thursday, August 18, 2005 1:13 PM To: Anders Nist?r Cc: emboss at emboss.open-bio.org Subject: Re: [EMBOSS] emma/clustalw PATH problems Anders Nist?r wrote: > Looking through the manual for emma there is a mention of > EMBOSS_CLUSTALW: > > "cannot find program 'clustalw'" - means that the ClustalW program has > not been set up on your site or is not in your environment (i.e. is > not on your path). The solutions are to (1) install clustalw in the > path so that emma can find it with the command "clustalw", or (2) > define a variable (an environment variable of in emboss.defaults or > your .embossrc file) called EMBOSS_CLUSTALW containing the command > (program name or full path) to run clustalw if you have it elsewhere > on your system. > > So I'm supposed to be able to specify the full path to clustalw > through EMBOSS_CLUSTALW.... > > Is the documentation wrong or is this a bug ? Ouch. It is a bug. The variable was originally set to allow older or newer versions of clustalw to be called. We have not tested programs that are not in the path. I am sure we can find a workaround for a fully specified path to the program. regards, Peter _______________________________________________ EMBOSS mailing list EMBOSS at emboss.open-bio.org http://newportal.open-bio.org/mailman/listinfo/emboss From andrespinzon at gmail.com Thu Aug 18 19:20:09 2005 From: andrespinzon at gmail.com (Andres Pinzon) Date: Thu, 18 Aug 2005 14:20:09 -0500 Subject: [EMBOSS] transfac site.dat ftp address In-Reply-To: <42F8C5A800003F7F@ms003msg.mail.fw> References: <42F8C5A800003F7F@ms003msg.mail.fw> Message-ID: <8968fc7e0508181220230e456b@mail.gmail.com> 2005/8/18, Dall'Olio Giovanni : > I was trying to use the 'tfscan' tool, but I can't find an ftp server to > download the 'site.dat' file that is required for this tool. Hi, as far as I know you are not supossed to download the database,(unless you are doing your own EMBOSS installation) you just have to define an input file and run the tool, thats it. The server which runs the tool should have the database already installed. Am I wrong? -- --------- Andr?s Pinz?n [http://www.andrespinzon.com] Bioinformatics Center, Colombia EMBnet node Biotechnology Institute - National University of Colombia http://bioinf.ibun.unal.edu.co Tel +57 3165000 ext 16961 Fax +571 3165415 ---------- From ajb at ebi.ac.uk Thu Aug 18 20:07:19 2005 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Thu, 18 Aug 2005 21:07:19 +0100 (BST) Subject: [EMBOSS] transfac site.dat ftp address In-Reply-To: <42F8C5A800003F7F@ms003msg.mail.fw> References: <42F8C5A800003F7F@ms003msg.mail.fw> Message-ID: <39657.81.96.71.66.1124395639.squirrel@webmail.ebi.ac.uk> The last free public version of transfac is on ftp://ftp.ebi.ac.uk/pub/databases/transfac/ (from memory) You can use the site.dat from that, write your own local version or pay the transfac people for the latest data. HTH Alan Bleasby EBI From emilywxu at yahoo.ca Thu Aug 18 23:28:11 2005 From: emilywxu at yahoo.ca (emily xu) Date: Thu, 18 Aug 2005 19:28:11 -0400 (EDT) Subject: [EMBOSS] needle qualifier Message-ID: <20050818232811.67700.qmail@web34011.mail.mud.yahoo.com> Hi there, I am new user and just installed the EMBOSS3.0.0 on UNIX. However, when I was trying to run program needle, I got the following error: UNIX % emboss/needle Needleman-Wunsch global alignment. Input sequence: query.1 Second sequence(s): target.1 Gap opening penalty [10.0]: 10.0 Gap extension penalty [0.5]: 0.5 Output alignment [ftsh_ecoli.needle]: ftsh_ecoli.needle Died: Qualifier '-bsequence' not found Why is it looking for '-bsequence'? The second sequence(s) have already been entered. Could someone help me with this? Thanks very much! Emily __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From David.Bauer at SCHERING.DE Fri Aug 19 05:34:42 2005 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Fri, 19 Aug 2005 07:34:42 +0200 Subject: [EMBOSS] Antwort: needle qualifier In-Reply-To: <20050818232811.67700.qmail@web34011.mail.mud.yahoo.com> Message-ID: I had a similar problem on a machine with some very old emboss libs hanging around. (in former time the parameter was named sequenceb and not bsequence) Make sure that you have only the current libajax, libajaxg and libnucleus in your search path for dynamic libraries. David. emboss-bounces at emboss.open-bio.org schrieb am 19/08/2005 01:28:11: > Hi there, > > I am new user and just installed the EMBOSS3.0.0 on > UNIX. However, when I was trying to run program > needle, I got the following error: > > UNIX % emboss/needle > Needleman-Wunsch global alignment. > Input sequence: query.1 > Second sequence(s): target.1 > Gap opening penalty [10.0]: 10.0 > Gap extension penalty [0.5]: 0.5 > Output alignment [ftsh_ecoli.needle]: > ftsh_ecoli.needle > Died: Qualifier '-bsequence' not found > > Why is it looking for '-bsequence'? The second > sequence(s) have already been entered. > Could someone help me with this? Thanks very much! > > Emily > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss From Sean.Maceachern at dpi.vic.gov.au Thu Aug 18 23:01:53 2005 From: Sean.Maceachern at dpi.vic.gov.au (Sean.Maceachern at dpi.vic.gov.au) Date: Fri, 19 Aug 2005 09:01:53 +1000 Subject: [EMBOSS] emma/clustalw PATH problems Message-ID: I have had a simillar problem with eprimer3, a temporary fix will be to modify your path so that it can find the clustalw binary eg) export PATH=$PATH:/home/sm82/primer3_1.0.0/src anders.nister at lcb.uu.se Sent by: To: emboss at emboss.open-bio.org emboss-bounces at emboss.o cc: pen-bio.org Subject: [EMBOSS] emma/clustalw PATH problems 19/08/2005 12:46 AM I am trying to run emma, and for certain reasons i don't have clustalw in my PATH. Running emma produces this error: EMBOSS An error in ajsys.c at line 398: cannot find program 'clustalw' Looking through the manual for emma there is a mention of EMBOSS_CLUSTALW: "cannot find program 'clustalw'" - means that the ClustalW program has not been set up on your site or is not in your environment (i.e. is not on your path). The solutions are to (1) install clustalw in the path so that emma can find it with the command "clustalw", or (2) define a variable (an environment variable of in emboss.defaults or your .embossrc file) called EMBOSS_CLUSTALW containing the command (program name or full path) to run clustalw if you have it elsewhere on your system. So I'm supposed to be able to specify the full path to clustalw through EMBOSS_CLUSTALW.... Setting this variable to the full path of clustalw produces a similar error to the one before. EMBOSS An error in ajsys.c at line 398: cannot find program '/usr/local/bin/clustalw' Looking through the emma source code I can see that ajSystemEnv is used to execute clustalw, this function will always look through the PATH env variable for the executable it is trying to run, so specifying a full path does absolutely nothing to get around the problem. Is the documentation wrong or is this a bug ? Has anyone got a workaround ? Is there any emboss function for executing an external program directly, without it being present in PATH ? /Anders Nist?r _______________________________________________ EMBOSS mailing list EMBOSS at emboss.open-bio.org http://newportal.open-bio.org/mailman/listinfo/emboss From ajb at ebi.ac.uk Fri Aug 19 09:15:48 2005 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Fri, 19 Aug 2005 10:15:48 +0100 (BST) Subject: [EMBOSS] needle qualifier In-Reply-To: <20050818232811.67700.qmail@web34011.mail.mud.yahoo.com> References: <20050818232811.67700.qmail@web34011.mail.mud.yahoo.com> Message-ID: <48138.81.96.71.66.1124442948.squirrel@webmail.ebi.ac.uk> To expand on the old library version issue: as of EMBOSS 3.0.0 we've started naming the ajax, ajaxg and nucleus libraries after the release number. So, the current library files will be called (e.g.) libajax.so.3.0.0 and there'll be symbolic links of libajax.so.3 and libajax.so to it. Any older libraries would probably be called (e.g.) libajax.so.1.0.0 or somesuch. HTH Alan From gbottu at ben.vub.ac.be Fri Aug 19 13:16:38 2005 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Fri, 19 Aug 2005 15:16:38 +0200 Subject: [EMBOSS] transfac site.dat ftp address In-Reply-To: <42F8C5A800003F7F@ms003msg.mail.fw> References: <42F8C5A800003F7F@ms003msg.mail.fw> Message-ID: <20050819131638.GA23671@bigben.ulb.ac.be> The file in the ftp server of the EBI is the last one that you could download just like that. If you like I can send you a copy of the site.dat version 4.0, less old but still from march 2000. This was the last academic users could get after signing a licence. In the mean time the ftp site has vanished and I do not think they will mind that I send you a copy, since it is still a very old file. The up-to-date version of TRANSFAC is only available against payment and not in the format suitable for standard EMBOSS and SRS. Regards, Guy Bottu, Belgian EMBnet Node From Andrew.Mather at dpi.vic.gov.au Sat Aug 20 01:38:24 2005 From: Andrew.Mather at dpi.vic.gov.au (Andrew.Mather at dpi.vic.gov.au) Date: Sat, 20 Aug 2005 11:38:24 +1000 Subject: [EMBOSS] emma/clustalw PATH problems Message-ID: Hi, You can also put a symlink in the directory with all the Emboss executables. I had to do this to get Emboss Explorer to work, even though both clustalw and primer3_core executables were in /usr/local/bin. I made a symlink in the Emboss-2.xxxx/bin directory and all was well. Andrew Bioinformatics Advanced Scientific Computing, Animal Genetics and Genomics, PIRVic Attwood 475 Mickleham Road, Attwood, 3049 ph +61 3 92174342 mob 0413 009 761 ---------------- There are 10 kinds of people...those who understand binary and those who don't. Sean.Maceachern at dpi.vic.gov.au Sent by: emboss-bounces at emboss.open-bio.org 19/08/05 09:01 AM To: anders.nister at lcb.uu.se cc: emboss at emboss.open-bio.org Subject: Re: [EMBOSS] emma/clustalw PATH problems I have had a simillar problem with eprimer3, a temporary fix will be to modify your path so that it can find the clustalw binary eg) export PATH=$PATH:/home/sm82/primer3_1.0.0/src anders.nister at lcb.uu.se Sent by: To: emboss at emboss.open-bio.org emboss-bounces at emboss.o cc: pen-bio.org Subject: [EMBOSS] emma/clustalw PATH problems 19/08/2005 12:46 AM I am trying to run emma, and for certain reasons i don't have clustalw in my PATH. Running emma produces this error: EMBOSS An error in ajsys.c at line 398: cannot find program 'clustalw' Looking through the manual for emma there is a mention of EMBOSS_CLUSTALW: "cannot find program 'clustalw'" - means that the ClustalW program has not been set up on your site or is not in your environment (i.e. is not on your path). The solutions are to (1) install clustalw in the path so that emma can find it with the command "clustalw", or (2) define a variable (an environment variable of in emboss.defaults or your .embossrc file) called EMBOSS_CLUSTALW containing the command (program name or full path) to run clustalw if you have it elsewhere on your system. So I'm supposed to be able to specify the full path to clustalw through EMBOSS_CLUSTALW.... Setting this variable to the full path of clustalw produces a similar error to the one before. EMBOSS An error in ajsys.c at line 398: cannot find program '/usr/local/bin/clustalw' Looking through the emma source code I can see that ajSystemEnv is used to execute clustalw, this function will always look through the PATH env variable for the executable it is trying to run, so specifying a full path does absolutely nothing to get around the problem. Is the documentation wrong or is this a bug ? Has anyone got a workaround ? Is there any emboss function for executing an external program directly, without it being present in PATH ? /Anders Nist?r _______________________________________________ EMBOSS mailing list EMBOSS at emboss.open-bio.org http://newportal.open-bio.org/mailman/listinfo/emboss _______________________________________________ EMBOSS mailing list EMBOSS at emboss.open-bio.org http://newportal.open-bio.org/mailman/listinfo/emboss From tjc at sanger.ac.uk Sat Aug 20 17:03:06 2005 From: tjc at sanger.ac.uk (Tim Carver) Date: Sat, 20 Aug 2005 18:03:06 +0100 (BST) Subject: [EMBOSS] emboss server In-Reply-To: <39102.129.111.174.49.1124381885.squirrel@biochem.uthscsa.edu> References: <39102.129.111.174.49.1124381885.squirrel@biochem.uthscsa.edu> Message-ID: Hi Jeremy Tomcat 5.5.* series will require Java 1.5. If you want to use java 1.4.2 you will need to use 5.0.28. So you will need to do a fresh install which means stopping tomcat and removing the tomcat, axis, and emboss installations. If you still have problems after re-installing check the tomcat logs ($TOMCAT/log/catalina.out) for error messages. Also ensure that you : -are running tomcat as the UID you define on installation -chown jembossctl to root and chmod u+s jembossctl. -ensure that the results directories are world read-writable. Hopefully this will help. Regards Tim Carver On Thu, 18 Aug 2005, Jeremy Mann wrote: > I still have not found the cure to my login problems with the EMBOSS > server. I've done the install several times now with and without > encryption, different kinds of authentication and nothing seems to work. > > With encryption selected I get: > No trusted certificate found > > I have done the encrypted install about a hundred times now and each time > it does make the certificate and I have edited the server.xml to reflect > the change. So I don't know what I'm missing here. > > Without encryption I don't get any errors, but the login prompt is always > popping up. I've tried all 6 types of authentication and none of them > work. > > I'm at my wits end and my head hurts from banging it on my desk ;) Could > somebody with a working Linux EMBOSS server contact me off or on list? > > Thanks a bunch! > > System: > Suse x86_64 9.1 > Java 1.4.2 > EMBOSS 3.0.0 > Latest Jemboss client > Tomcat 5.5.9 with compat library > Axis 1_2 > > > > -- > Jeremy Mann > jeremy at biochem.uthscsa.edu > > University of Texas Health Science Center > Bioinformatics Core Facility > http://www.bioinformatics.uthscsa.edu > Phone: (210) 567-2672 > > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss > The Wellcome Trust Sanger Institute Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK From smiddha at indiana.edu Sun Aug 21 05:12:21 2005 From: smiddha at indiana.edu (Sumit Middha) Date: Sun, 21 Aug 2005 00:12:21 -0500 Subject: [EMBOSS] emboss-explorer post installation In-Reply-To: References: Message-ID: <1124601141.43080d3568207@webmail.iu.edu> Hello Andrew, Thanks so much for your response. Probably I did not focus my question properly. Yes I did manage to install using the script, and specified the paths. However, I could not figure out, what my server should point to (I guess the index page in html). Also I am unsure of how the emboss installation gets linked to the explorer (I dont think I mentioned it anywhere during the installation of this emboss-explorer). And do you have or know of any comparisons, betwween emboss interfaces from w2h, pise and emboss-explorer ? Cheers, Sumit Quoting Andrew.Mather at dpi.vic.gov.au: > Hi Sumit, > > No, I don't really have any notes, because the installation is very > straightforward. > > The only thing I had to do was to edit the install script to point to my > perl binary, which is in /usr/local/bin, not /usr/bin. Once I did that > and ran the script, everything 'just worked', except for the clustal and > primer3_core issue. > > That was fixed by making a symbolic link in my Emboss bin directory to the > clustalw and primer3_core executables. Other than that, there was no > problem. > > When you run the script, it asks you where the various directories are and > installs things wherever you tell it. The only thing I'm not sure of is > if you need to have bioPerl installed beforehand. > > Because we have, it didn't ask about it, so I'm not sure. > > I did have quite a few problems with the previous version of > Emboss-explorer, which was called Emboss::GUI, however upgrading to the > current version removed all of those. > > Andrew > > > > Bioinformatics Advanced Scientific Computing, > Animal Genetics and Genomics, PIRVic Attwood > 475 Mickleham Road, Attwood, 3049 > ph +61 3 92174342 > mob 0413 009 761 > > > ---------------- > There are 10 kinds of people...those who understand binary and those who > don't. > > > > > > smiddha at indiana.edu > 20/08/05 02:20 PM > > > To: Andrew.Mather at dpi.vic.gov.au > cc: > Subject: Re: [EMBOSS] emma/clustalw PATH problems > > > > Hello Andrew, > Do you have notes on installation of Emboss-explorer? It would be great > help to > look at those for my installation. > > Thanks, > Sumit > > > Quoting Andrew.Mather at dpi.vic.gov.au: > > > Hi, > > > > You can also put a symlink in the directory with all the Emboss > > executables. > > > > I had to do this to get Emboss Explorer to work, even though both > clustalw > > and primer3_core executables were in /usr/local/bin. > > > > I made a symlink in the Emboss-2.xxxx/bin directory and all was well. > > > > Andrew > > > > > > > > Bioinformatics Advanced Scientific Computing, > > Animal Genetics and Genomics, PIRVic Attwood > > 475 Mickleham Road, Attwood, 3049 > > ph +61 3 92174342 > > mob 0413 009 761 > > > > > > ---------------- > > There are 10 kinds of people...those who understand binary and those who > > > don't. > > > > > > > > > > > > Sean.Maceachern at dpi.vic.gov.au > > Sent by: emboss-bounces at emboss.open-bio.org > > 19/08/05 09:01 AM > > > > > > To: anders.nister at lcb.uu.se > > cc: emboss at emboss.open-bio.org > > Subject: Re: [EMBOSS] emma/clustalw PATH problems > > > > > > > > I have had a simillar problem with eprimer3, a temporary fix will be to > > modify your path so that it can find the clustalw binary > > > > eg) > > > > export PATH=$PATH:/home/sm82/primer3_1.0.0/src > > > > > > > > > > > > > > anders.nister at lcb.uu.se > > Sent by: To: > > emboss at emboss.open-bio.org > > emboss-bounces at emboss.o cc: > > pen-bio.org Subject: [EMBOSS] > > emma/clustalw PATH problems > > > > > > 19/08/2005 12:46 AM > > > > > > > > > > > > > > I am trying to run emma, and for certain reasons i don't have clustalw > in > > my > > PATH. > > > > Running emma produces this error: > > > > EMBOSS An error in ajsys.c at line 398: > > cannot find program 'clustalw' > > > > > > Looking through the manual for emma there is a mention of > EMBOSS_CLUSTALW: > > > > "cannot find program 'clustalw'" - means that the ClustalW program > has > > not been set up on your site or is not in your environment (i.e. is > > not on your path). The solutions are to (1) install clustalw in the > > path so that emma can find it with the command "clustalw", or (2) > > define a variable (an environment variable of in emboss.defaults or > > your .embossrc file) called EMBOSS_CLUSTALW containing the command > > (program name or full path) to run clustalw if you have it elsewhere > > on your system. > > > > So I'm supposed to be able to specify the full path to clustalw through > > EMBOSS_CLUSTALW.... > > > > Setting this variable to the full path of clustalw produces a similar > > error > > to the one before. > > > > EMBOSS An error in ajsys.c at line 398: > > cannot find program '/usr/local/bin/clustalw' > > > > Looking through the emma source code I can see that ajSystemEnv is used > to > > execute clustalw, this function will always look through the PATH env > > variable for the executable it is trying to run, so specifying a full > path > > does absolutely nothing to get around the problem. > > > > Is the documentation wrong or is this a bug ? > > Has anyone got a workaround ? > > Is there any emboss function for executing an external program directly, > > without it being present in PATH ? > > > > /Anders Nist?r > > > > _______________________________________________ > > EMBOSS mailing list > > EMBOSS at emboss.open-bio.org > > http://newportal.open-bio.org/mailman/listinfo/emboss > > > > > > > > > > > > > > _______________________________________________ > > EMBOSS mailing list > > EMBOSS at emboss.open-bio.org > > http://newportal.open-bio.org/mailman/listinfo/emboss > > > > > > > > _______________________________________________ > > EMBOSS mailing list > > EMBOSS at emboss.open-bio.org > > http://newportal.open-bio.org/mailman/listinfo/emboss > > > > > From pmr at ebi.ac.uk Mon Aug 22 06:50:32 2005 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Mon, 22 Aug 2005 07:50:32 +0100 (BST) Subject: [EMBOSS] emboss-explorer post installation In-Reply-To: <1124601141.43080d3568207@webmail.iu.edu> References: <1124601141.43080d3568207@webmail.iu.edu> Message-ID: <1289.172.203.254.24.1124693432.squirrel@webmail.ebi.ac.uk> Dear Sumit, > And do you have or know of any comparisons, between emboss interfaces > from w2h, > pise and emboss-explorer ? I plan to send a survey to all the EMBOSS interfaces so that we can make a comparison on the EMBOSS website. This will take a little time to organise. So, does anyone already have a comparison? It would be helpful when I write the survey form. regards, Peter Rice From golharam at umdnj.edu Mon Aug 22 20:57:06 2005 From: golharam at umdnj.edu (Ryan Golhar) Date: Mon, 22 Aug 2005 16:57:06 -0400 Subject: [EMBOSS] Emma in EMBOSS Explorer Message-ID: <021201c5a75c$0e3a0380$2f01a8c0@GOLHARMOBILE1> In EMBOSS Explorer, using EMMA, one of the options under Slow align options is "Do you want to carry out slow or fast pairwise alignment? The options available is "Yes/No". Shouldn't that be slow/fast? -- Ryan Golhar - golharam at umdnj.edu The Informatics Institute of UMDNJ 973-972-5034 From rob.pollock at gmail.com Tue Aug 23 03:34:07 2005 From: rob.pollock at gmail.com (Rob Pollock) Date: Tue, 23 Aug 2005 15:34:07 +1200 Subject: [EMBOSS] Long Refseq accessions and dbifasta/seqret bug?? Message-ID: Hi, I download human.protein.faa from NCBI on a weekly basis and use dbifasta to build an emboss database. However, I have recently noticed that seqret has problems finding sequences with certain accessions, even though they are in the database. I suspect this is something to do with the new long RefSeq accessions and the way the index is built. Here is an example: (I call my RefSeq protein database 'genprot' for want of a better name) I am using EMBOSS 3.0.0 btw. (also Version 2.10.0 did the same thing) This fails: % seqret 'genprot:NP_001015.1' Reads and writes (returns) sequences Error: Unable to read sequence 'genprot:NP_001015.1' Died: seqret terminated: Bad value for '-sequence' and no prompt However this works: % seqret 'genprot:NP_001015' Reads and writes (returns) sequences Output sequence [np_001015.fasta]: % more np_001015.fasta >NP_001015.1 NP_001015.1 ribosomal protein S21 [Homo sapiens] MQNDAGEFVDLYVPRKCSASNRIIGAKDHASIQMNVAEVDKVTGRFNGQFKTYAICGAIR RMGESDDSILRLAKADGIVSKNF If I search human.protein.faa for strings that match NP_0010150 get a whole list: >gi|62632744|ref|NP_001015050.1| hypothetical protein LOC200810 [Homo sapiens] >gi|62821803|ref|NP_001015884.1| RPB11b2alpha protein [Homo sapiens] >gi|62865862|ref|NP_001015508.1| purine-rich element binding protein G isoform B [Homo sapiens] >gi|62865641|ref|NP_001015879.1| aurora kinaseatching NP_001015 I get a whole list: ... etc Again, using the full accession for any one of these fails: % seqret 'genprot:NP_001015071.1' Reads and writes (returns) sequences Error: Unable to read sequence 'genprot:NP_001015071.1' Died: seqret terminated: Bad value for '-sequence' and no prompt But, again, the truncated accession works: % seqret 'genprot:NP_001015071' Reads and writes (returns) sequences Output sequence [np_001015071.fasta]: Other sequences searched by full accession work fine (as long as they're _in_ the database!) % seqret 'genprot:NP_000544.1' Reads and writes (returns) sequences Output sequence [np_000544.fasta]: I think the long accessions are calling dbifasta/seqret to spit the dummy somehow. Note:This is how I format my database % dbifasta -dbname genprot -idformat ncbi -directory ~/genprot -filenames \*.faa -auto Maybe there is a workaround at this point?? Any suggestions?? [I have a file that includes sequences I need that aren't found in the current release of Refseq which is diff.faa, hence the -filenames \*.faa bit.] Thanks in advance Rob Pollock. From fernan at iib.unsam.edu.ar Tue Aug 23 12:56:13 2005 From: fernan at iib.unsam.edu.ar (Fernan Aguero) Date: Tue, 23 Aug 2005 09:56:13 -0300 Subject: [EMBOSS] Emma in EMBOSS Explorer In-Reply-To: <021201c5a75c$0e3a0380$2f01a8c0@GOLHARMOBILE1> References: <021201c5a75c$0e3a0380$2f01a8c0@GOLHARMOBILE1> Message-ID: <20050823125613.GJ15503@iib.unsam.edu.ar> +----[ Ryan Golhar (22.Aug.2005 18:17): | | In EMBOSS Explorer, using EMMA, one of the options under Slow align | options is "Do you want to carry out slow or fast pairwise alignment? | The options available is "Yes/No". Shouldn't that be slow/fast? | +----] In my particular view or reading of the meaning of the question I would say that if the question was "What kind (or speed) of pairwise alignment do you want?" then the options could be "Slow/Fast". But the question is just asking you to say Yes or No to whether you want something (a slow or fast alignment) or not. Anyway, EMMA is just a wrapper around clustalw. And that option comes from good ol' clustalw. So if you want it changed, I guess you have to bug the original authors ... But in the end (and apologies in advance since I know this is foreign to the EMBOSS culture/tradition), it doesn't really matter what colour we paint the bikeshed: http://www.freebsd.org/doc/en_US.ISO8859-1/books/faq/misc.html#BIKESHED-PAINTING Fernan From rob.pollock at gmail.com Wed Aug 24 05:22:47 2005 From: rob.pollock at gmail.com (Rob Pollock) Date: Wed, 24 Aug 2005 17:22:47 +1200 Subject: [EMBOSS] Long Refseq accessions and dbifasta/seqret bug?? SOLVED.. workaround In-Reply-To: References: Message-ID: Ok, well if you use dbxfasta and define a "resource" with sufficiently long (id and acc) fields, it works. % tfm dbxfasta for what I mean by resource On 8/23/05, Rob Pollock wrote: > Hi, > > I download human.protein.faa from NCBI on a weekly basis and use dbifasta to > build an emboss database. However, I have recently noticed that > seqret has problems > finding sequences with certain accessions, even though they are in the database. > > I suspect this is something to do with the new long RefSeq accessions > and the way > the index is built. Here is an example: (I call my RefSeq protein > database 'genprot' for > want of a better name) > > I am using EMBOSS 3.0.0 btw. (also Version 2.10.0 did the same thing) > > This fails: > > % seqret 'genprot:NP_001015.1' > Reads and writes (returns) sequences > Error: Unable to read sequence 'genprot:NP_001015.1' > Died: seqret terminated: Bad value for '-sequence' and no prompt > > However this works: > % seqret 'genprot:NP_001015' > Reads and writes (returns) sequences > Output sequence [np_001015.fasta]: > > % more np_001015.fasta > >NP_001015.1 NP_001015.1 ribosomal protein S21 [Homo sapiens] > MQNDAGEFVDLYVPRKCSASNRIIGAKDHASIQMNVAEVDKVTGRFNGQFKTYAICGAIR > RMGESDDSILRLAKADGIVSKNF > > If I search human.protein.faa for strings that match NP_0010150 get a > whole list: > > >gi|62632744|ref|NP_001015050.1| hypothetical protein LOC200810 [Homo sapiens] > >gi|62821803|ref|NP_001015884.1| RPB11b2alpha protein [Homo sapiens] > >gi|62865862|ref|NP_001015508.1| purine-rich element binding protein G > isoform B [Homo sapiens] > >gi|62865641|ref|NP_001015879.1| aurora kinaseatching NP_001015 I get > a whole list: > ... etc > > Again, using the full accession for any one of these fails: > > % seqret 'genprot:NP_001015071.1' > Reads and writes (returns) sequences > Error: Unable to read sequence 'genprot:NP_001015071.1' > Died: seqret terminated: Bad value for '-sequence' and no prompt > > But, again, the truncated accession works: > % seqret 'genprot:NP_001015071' > Reads and writes (returns) sequences > Output sequence [np_001015071.fasta]: > > Other sequences searched by full accession work fine (as long as > they're _in_ the > database!) > > % seqret 'genprot:NP_000544.1' > Reads and writes (returns) sequences > Output sequence [np_000544.fasta]: > > I think the long accessions are calling dbifasta/seqret to spit the > dummy somehow. > > Note:This is how I format my database > > % dbifasta -dbname genprot -idformat ncbi -directory ~/genprot > -filenames \*.faa -auto > > Maybe there is a workaround at this point?? Any suggestions?? > > [I have a file that includes sequences I need that aren't found in the current > release of Refseq which is diff.faa, hence the -filenames \*.faa bit.] > > Thanks in advance > Rob Pollock. > From dalloliogm at gmail.com Wed Aug 24 19:21:08 2005 From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio) Date: Wed, 24 Aug 2005 21:21:08 +0200 Subject: [EMBOSS] embossrc - configure database NPRD and AEdb Message-ID: <5aa3b3570508241221142887a8@mail.gmail.com> Hi all, I'm trying to configure this two databases in my .embossrc - emboss_default , but I didn't managed to get it works: http://srs6.bionet.nsc.ru/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+3Xn_71Qks76+-lib+NUCLEOSOME http://www.ebi.ac.uk/asd-srv/AEdb-query.cgi?method=MAIN&visit=first For the first one, I've tried this: DB NPRD [ method: srswww format: embl # url: " http://srs6.bionet.nsc.ru/srs6bin/cgi-bin/wgetz?-id+1YUkq1Qk6fN+-e+[NUCLEOSOME:'%s'] " # url: " http://srs6.bionet.nsc.ru/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+3Xn_71QkMvb+-lib+NUCLEOSOME " # url: " http://srs6.bionet.nsc.ru/srs6bin/cgi-bin/wgetz?-id+-e+[NUCLEOSOME:'%s']" url: "http://srs6.bionet.nsc.ru/srs6bin/cgi-bin/wgetz" type: N dbalias: NUCLEOSOME app: getz fields: "AC SQ" ] But what's is wrong? How can I understand what is the 'correct' url to choose, and how can I determine the right 'method' and 'format'? I've seen that in the main page of this database, there are description about the syntax and the and the structure in SRS. For example, can I use the informations described here: http://srs6.bionet.nsc.ru/srs6bin/cgi-bin/wgetz?-page+icarusFile+-id+3Xn_71Qks76+-l+NUCLEOSOME+-ifile+i? Thank you for any reply. Giovanni -- ----------------------------------------------------------- Visit my website! http://dalloliogm.altervista.org From ulrike.kaule at gmx.de Wed Aug 24 20:22:11 2005 From: ulrike.kaule at gmx.de (Ulrike Kaule) Date: Wed, 24 Aug 2005 22:22:11 +0200 Subject: [EMBOSS] output of program "digest" as input for program "pepstats" ? Message-ID: <430CD6F3.30306@gmx.de> Hello, I'm a new user to emboss. Within a Taverna-Workflow I want to digest a protein-sequence first with the emboss-program "digest" and to use the output of "digest" - the seqtable with the fragments - as an input for further sequence-analysis programs. So the resulting fragments should be analysed by pepstats or iep. But I have problems with the connection of these programs, because the output of "digest" is not accepted by the other programs as input. I thougth to solve this problem with using "seqret" between "digest" and "pepstats", but this doesn't work. Is there any solution to extract the protein-fragments produced by "digest" and to use them as input for other programs? Thank you in advance Ulrike From s_y_jeong at yahoo.com Thu Aug 25 00:24:56 2005 From: s_y_jeong at yahoo.com (Seong-Yun Jeong) Date: Wed, 24 Aug 2005 17:24:56 -0700 (PDT) Subject: [EMBOSS] Please remove my address Message-ID: <20050825002456.66798.qmail@web34015.mail.mud.yahoo.com> I don't want to get these mails. Please remove my address from the list. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From gbottu at ben.vub.ac.be Thu Aug 25 12:18:43 2005 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Thu, 25 Aug 2005 14:18:43 +0200 Subject: [EMBOSS] output of program "digest" as input for program "pepstats" ? In-Reply-To: <430CD6F3.30306@gmx.de> References: <430CD6F3.30306@gmx.de> Message-ID: <20050825121843.GA5549@bigben.ulb.ac.be> Dear Ulrike, You can ask digest for a "Report Format" of type "List File", which you can give as input to pepstats or iep (the peptides will be analyzed as individual sequences and the results given the one aftert the other, they are not merged). I have no experience with Taverna and hence cannot tell you exactly how to. I know that at the command line you would have to : digest mysequence -rformat=listfile -outfile=myreport iep list::myreport Regards, Guy Bottu, Belgian EMBnet Node From lukem at gene.pbi.nrc.ca Fri Aug 26 19:16:40 2005 From: lukem at gene.pbi.nrc.ca (Luke McCarthy) Date: Fri, 26 Aug 2005 13:16:40 -0600 Subject: [EMBOSS] emboss-explorer post installation In-Reply-To: <1124601141.43080d3568207@webmail.iu.edu> References: <1124601141.43080d3568207@webmail.iu.edu> Message-ID: <1125083799.6666.12.camel@incognito.invalid> On Sat, 2005-08-20 at 23:12, Sumit Middha wrote: > Hello Andrew, > Thanks so much for your response. Probably I did not focus my question properly. > Yes I did manage to install using the script, and specified the paths. > > However, I could not figure out, what my server should point to (I guess the > index page in html). At the end of the install script, there is a message containing some important information. One such piece of information is the URL to access the EMBOSS explorer interface. It says something like "Visit URL_TO_EMBOSS_EXPLORER to test it out." That's the URL you should use. The url you should use is the url to the CGI script (usually something like http://hostname/cgi-bin/emboss) > Also I am unsure of how the emboss installation gets linked > to the explorer (I dont think I mentioned it anywhere during the > installation of this emboss-explorer). I'm afraid I don't understand the question. The questions you answer during the install script provide all of the information EMBOSS explorer needs to find the EMBOSS installation. If you need to change this information at a later date, you can either re-run the install script, or edit the configuration module (the location of which is provided in the message at the end of the install script...) Cheers, Luke From smiddha at indiana.edu Mon Aug 29 21:30:15 2005 From: smiddha at indiana.edu (Sumit Middha) Date: Mon, 29 Aug 2005 16:30:15 -0500 Subject: [EMBOSS] emboss-explorer in non-default directory In-Reply-To: <1125083799.6666.12.camel@incognito.invalid> References: <1124601141.43080d3568207@webmail.iu.edu> <1125083799.6666.12.camel@incognito.invalid> Message-ID: <1125351015.43137e67ebdc2@webmail.iu.edu> Thanks Luke. Yes I figured that out. However, I get an error in the menu frame, when I open the emboss-explorer. Died: Qualifier '-showembassy' not found, referer: http://bioportal/cgi-bin/emboss/menu [Mon Aug 29 16:22:11 2005] [error] [client 156.56.96.41] , referer: http://bioportal/cgi-bin/emboss/menu [Mon Aug 29 16:22:11 2005] [error] [client 156.56.96.41] Can't use an undefined value as an ARRAY reference at /bioportal/web/tools/emboss-explorer/lib/EMBOSS/GUI/XHTML.pm line 317., referer: http://bioportal/cgi-bin/emboss/menu I am trying to fix this by making changes, but your help will be valuable. Quoting Luke McCarthy : > On Sat, 2005-08-20 at 23:12, Sumit Middha wrote: > > Hello Andrew, > > Thanks so much for your response. Probably I did not focus my question > properly. > > Yes I did manage to install using the script, and specified the paths. > > > > However, I could not figure out, what my server should point to (I > guess the > > index page in html). > > At the end of the install script, there is a message containing some > important information. One such piece of information is the URL to > access the EMBOSS explorer interface. It says something like "Visit > URL_TO_EMBOSS_EXPLORER to test it out." That's the URL you should use. > > The url you should use is the url to the CGI script (usually something > like http://hostname/cgi-bin/emboss) > > > Also I am unsure of how the emboss installation gets linked > > to the explorer (I dont think I mentioned it anywhere during the > > installation of this emboss-explorer). > > I'm afraid I don't understand the question. The questions you answer > during the install script provide all of the information EMBOSS explorer > needs to find the EMBOSS installation. If you need to change this > information at a later date, you can either re-run the install script, > or edit the configuration module (the location of which is provided in > the message at the end of the install script...) > > Cheers, > > Luke > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss > From golharam at umdnj.edu Tue Aug 30 04:20:37 2005 From: golharam at umdnj.edu (Ryan Golhar) Date: Tue, 30 Aug 2005 00:20:37 -0400 Subject: [EMBOSS] NCBI Blast in emboss-explorer Message-ID: <005501c5ad1a$2e1b6770$d33d140a@GOLHARMOBILE1> Has anyone tried incorporating NCBI Blast into the emboss-explorer UI? I haven't read the documentation yet on how to incorporate other applications into EMBOSS, as I was hoping someone else has already done this with BLAST :) Ryan From lukem at gene.pbi.nrc.ca Tue Aug 30 05:28:37 2005 From: lukem at gene.pbi.nrc.ca (Luke McCarthy) Date: Mon, 29 Aug 2005 23:28:37 -0600 Subject: [EMBOSS] NCBI Blast in emboss-explorer In-Reply-To: <005501c5ad1a$2e1b6770$d33d140a@GOLHARMOBILE1> References: <005501c5ad1a$2e1b6770$d33d140a@GOLHARMOBILE1> Message-ID: <1125379717.6049.12.camel@drmemory.private.virtuouspagans.org> On Mon, 2005-08-29 at 22:20, Ryan Golhar wrote: > Has anyone tried incorporating NCBI Blast into the emboss-explorer UI? > > I haven't read the documentation yet on how to incorporate other > applications into EMBOSS, as I was hoping someone else has already done > this with BLAST :) I don't know precisely what else is required to create an EMBOSS wrapper (a la emma) around an external program, but if your only concern is EMBOSS explorer, all you have to do is mock up an ACD file with the same name as the executable (in the same location as the other EMBOSS ACD files, usually /usr/local/share/EMBOSS/acd/ or something similar) and make sure the executable is in the EMBOSS explorer PATH (set in the configuration module, but by default it's the location of the EMBOSS binaries...) In the ACD file, the name of each parameter has to be the command line switch. For example: datafile: i [ required: "y" ] outfile: o [ required: "y" ] For best results, you'd have to put the options in appropriate sections, etc. The only tricky part I can see is that you'd have to hardcode your available BLAST databases in the ACD file. It's entirely possible that someone has already done this, or has written an actual EMBOSS wrapper for BLAST. If there is no such response forthcoming, I'll whip up a blastall.acd later this week and put it up on the EMBOSS explorer website. It would be a good way to showcase the flexibility of the interface and the ACD language itself. Cheers, Luke From ajb at ebi.ac.uk Tue Aug 30 07:28:55 2005 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Tue, 30 Aug 2005 08:28:55 +0100 (BST) Subject: [EMBOSS] NCBI Blast in emboss-explorer In-Reply-To: <1125379717.6049.12.camel@drmemory.private.virtuouspagans.org> References: <005501c5ad1a$2e1b6770$d33d140a@GOLHARMOBILE1> <1125379717.6049.12.camel@drmemory.private.virtuouspagans.org> Message-ID: <37186.172.31.70.99.1125386935.squirrel@webmail.ebi.ac.uk> Wrapping BLAST is on our things to do list for the medium term. I believe at least two sites have attempted this in the past. At the low level this is best done by splitting blastall into separate applications as it fits better with exposing them as web/GRID services. The blastall functionality can then be implemented as a GUI layer. As for the short term, we'll be watching with interest! Alan From gbottu at ben.vub.ac.be Tue Aug 30 10:17:57 2005 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Tue, 30 Aug 2005 12:17:57 +0200 Subject: [EMBOSS] NCBI BLAST under EMBOSS Message-ID: <20050830101757.GA10712@bigben.ulb.ac.be> Dear Ryan, dear all, You can download from http://www.wemboss.org/ wrappers4EMBOSS, which allows to access BLAST (as well as some other software) from under EMBOSS (as the standard distribution of EMBOSS already does for CLUSTAL and Primer3). Note by the way that an article about it appeared in EMBnet.news 11(1) (see http://www.embnet.org/download/embnetnews/). Some further remarks : - Just putting the blastall program in the EMBOSS .../bin directory and writing a blastall.acd file will not work well (only fastA format query sequence accepted, need to write absolute path to databanks in ACD file since the Web interface has no BLASTDB shell environment variable, etc.). Better is to write an EMBOSS "wrapper" program that starts by reading the ACD file and does whatever else is needed. Our "wrapper" can, among other things, generate on-the-fly from a List of sequences a databank to be searched. - Our "wrapper" works well in a terminal and under wEMBOSS. Since the ACD syntax is quite complex it does not run well under all GUI's. I know that the old EMBOSS-GUI of Luke did not manage well the hide/unhide of the parameters. I do not know how EMBOSS Explorer works ; I would like to hear about it as soon as somebody tested. To make BLAST work under all GUI's it might, as proposed, be needed to make separate programs for blastn, blastp, etc. - The databanks are indeed a problem. An EMBOSS library module that can find the databanks (as exists in GCG) would be nice. In the mean time, our wrappers need the databank names in the ACD files. As you will see if you try, wrappers4EMBOSS asks for the names of the databanks when you install it. A problem is that whenever you change the collection of databanks on your site you need to do the installation again or edit manually the ACD files. Hope this helps, Guy Bottu, Belgian EMBnet Node