From jmuehlis at uni-muenster.de Mon May 9 10:33:25 2005 From: jmuehlis at uni-muenster.de (Joerg Muehlisch) Date: Mon, 9 May 2005 16:33:25 +0200 Subject: [EMBOSS] emboss installation Message-ID: <200505091633.25818.jmuehlis@uni-muenster.de> Hi over there. I am just trying to install Emboss again, now under SUSE 9.2. After installing the package xdevel, that I found out to be needed, configure stops here and I can not find out how to solve this: EMBOSS-2.10.0> ./configure checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for gawk... (cached) gawk checking for gcc... cpp checking for C compiler default output file name... b.out checking whether the C compiler works... configure: error: cannot runC compiled programs. If you meant to cross compile, use `--host'. See `config.log' for more details. May be somebody ran into the same problem or knows how to solve this anyway. I did not have this problem the last time or easily found the solution... So thanks for your help, Jorg Muhlisch a user From simon.andrews at bbsrc.ac.uk Tue May 10 03:29:01 2005 From: simon.andrews at bbsrc.ac.uk (simon andrews (BI)) Date: Tue, 10 May 2005 08:29:01 +0100 Subject: [EMBOSS] emboss installation In-Reply-To: <200505091633.25818.jmuehlis@uni-muenster.de> References: <200505091633.25818.jmuehlis@uni-muenster.de> Message-ID: <1caeeea0856ae5ea9428290325f16922@bbsrc.ac.uk> On 9 May 2005, at 15:33, Joerg Muehlisch wrote: > Hi over there. > > I am just trying to install Emboss again, now under SUSE 9.2. After > installing > the package xdevel, that I found out to be needed, configure stops > here and I > can not find out how to solve this: > > EMBOSS-2.10.0> ./configure > checking for a BSD-compatible install... /usr/bin/install -c > checking whether build environment is sane... yes > checking for gawk... gawk > checking whether make sets $(MAKE)... yes > checking for gawk... (cached) gawk > checking for gcc... cpp This looks wrong. Configure is looking for gcc (a c compiler) but is getting cpp (the C preprocessor). You should install gcc and try to run configure again. If gcc is already installed then check that your CC environment variable hasn't been set to something odd as this will override the autodetection of the c compiler in configure. Simon. -- Simon Andrews PhD Bioinformatics Dept. The Babraham Institute simon.andrews at bbsrc.ac.uk +44 (0) 1223 496463 From cquijano at iib.uam.es Tue May 10 04:54:04 2005 From: cquijano at iib.uam.es (Carlos Quijano) Date: Tue, 10 May 2005 10:54:04 +0200 Subject: [EMBOSS] emboss installation In-Reply-To: <1caeeea0856ae5ea9428290325f16922@bbsrc.ac.uk> References: <200505091633.25818.jmuehlis@uni-muenster.de> <1caeeea0856ae5ea9428290325f16922@bbsrc.ac.uk> Message-ID: <1115715244.9058.37.camel@furthermore.iib.uam.es> Perhaps I will go a little bit out of the thread, but as excange I give some ideas related with it first, and then I say what I actually want to share/advice. With the simple output of ./configure is not possible to know how exactly happens your crash, and I will give no more info than Simon. But I suspect that the problem is in your development libraries (you miss something). Do what the crash-output tells you and study the installation "log", if necessary, use special verbose options in ./configure to investigate further. Luck! As far as I know, there are not current binaries for v2.10, so perhaps it is the reason for you to compile the sources. I suposse anyway that Gentoo will provide v2.10 Emboss sources soon and then you would only need to use Gentoo. (http://packages.gentoo.org/search/?sstring=emboss) You can even try to install emboss 2.10 gentoo sources right now, having in mind that you would have to unmask it from portage because it is in testing phase by this very moment. I love to compile and patch from sources... Gentoo is great for this! Debian too. If you are to habitually compile lots of packages by yourself I recommend you Gentoo. If not, Debian, that you can install from binaries easier and afterwards some packages from source when you need it. Currently, I am a happy man with Gentoo. My workstation is now my friend, not my nightmare. And I dont need to get crazy before planning a whole system upgrade, and neither after... I only wanted to share my happiness, sorry for the somewhat offtopic mail... :D Carlos. El mar, 10-05-2005 a las 08:29 +0100, simon andrews escribi?: > On 9 May 2005, at 15:33, Joerg Muehlisch wrote: > > > Hi over there. > > > > I am just trying to install Emboss again, now under SUSE 9.2. After > > installing > > the package xdevel, that I found out to be needed, configure stops > > here and I > > can not find out how to solve this: > > > > EMBOSS-2.10.0> ./configure > > checking for a BSD-compatible install... /usr/bin/install -c > > checking whether build environment is sane... yes > > checking for gawk... gawk > > checking whether make sets $(MAKE)... yes > > checking for gawk... (cached) gawk > > checking for gcc... cpp > > This looks wrong. Configure is looking for gcc (a c compiler) but is > getting cpp (the C preprocessor). You should install gcc and try to > run configure again. > > If gcc is already installed then check that your CC environment > variable hasn't been set to something odd as this will override the > autodetection of the c compiler in configure. > > Simon. From jmuehlis at uni-muenster.de Tue May 10 05:40:46 2005 From: jmuehlis at uni-muenster.de (Joerg Muehlisch) Date: Tue, 10 May 2005 11:40:46 +0200 Subject: [EMBOSS] Installation Message-ID: <200505101140.46471.jmuehlis@uni-muenster.de> Hello, I knew it would be a very simple silly mistake..., but I could not find it. Know having the compiler installed in fact it works working fine. I just remember the last time I installed there was a SUSE specific compiler that was not called gcc and was not found by configure, so I remember I had to introduce it as recommended in the script and this time I chose CC= cpp, what is obviously wrong. So I am very sorry to bother you with a simple problem like that. May be it would be a good idea to add these hints for the "users" wanting to install emboss on SUSE 9.2: 1. Install xdev package xdevel (not to find with xdev in Yast) 2. Install gcc (in former versions of SUSE this was standard) 3. Set a path variable for the libs in /usr/locale/lib?, because: >wossname wossname: error while loading shared libraries: libnucleus.so.0: cannot open shared object file: No such file or directory What would be the correct place to define that? I know this is more linux than emboss question, but as a simple user... I hope that anybody can help me with this last point, so that I will be able to work with start working with emboss again. I d like to thank everybody who is helping with this software, as it is very useful to me. I thank everybody for the help and apologize for the inconveniences. Jorg Muhlisch off topic: I m just used to work with SUSE... so it is the easiest way to me. From jmuehlis at uni-muenster.de Tue May 10 06:06:41 2005 From: jmuehlis at uni-muenster.de (Joerg Muehlisch) Date: Tue, 10 May 2005 12:06:41 +0200 Subject: [EMBOSS] emboss installation Message-ID: <200505101206.41413.jmuehlis@uni-muenster.de> Hello, I was to fast again in submitting my problem. After a restart everything works fine. Maybe the variables were not acualized for this console window... Thanks anyway for the help Jorg Muhlisch From andrespinzon at gmail.com Tue May 10 13:26:34 2005 From: andrespinzon at gmail.com (Andres Pinzon) Date: Tue, 10 May 2005 12:26:34 -0500 Subject: [EMBOSS] Installation In-Reply-To: <200505101140.46471.jmuehlis@uni-muenster.de> References: <200505101140.46471.jmuehlis@uni-muenster.de> Message-ID: <8968fc7e05051010265b436a4@mail.gmail.com> 2005/5/10, Joerg Muehlisch : > Hello, > wossname: error while loading shared libraries: libnucleus.so.0: cannot open > shared object file: No such file or directory > What would be the correct place to define that? > I know this is more linux than emboss question, but as a simple user... if im not wrong, libnucleus is part of the EMBOSS installation, and it should be in /usr/local/emboss/lib if u installed emboss in that path. > off topic: > I m just used to work with SUSE... so it is the easiest way to me. Hey, dont worry about that, i have 2 emboss installations in SUSE9.2 and it works just fine!!!! At home I use Slackware, but at my Job Im in charge of 4 machines and 3 of them run SUSE, it rocks anyway. -- --------- Andr?s Pinz?n [http://www.andrespinzon.com] Centro de Bioinformatica, Instituto de Biotecnologia http://bioinf.ibun.unal.edu.co Universidad Nacional de Colombia tel. 3165000 ext. 16961 GNU/Linux user number 349752 ---------- From gbottu at ben.vub.ac.be Wed May 18 12:35:56 2005 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Wed, 18 May 2005 18:35:56 +0200 Subject: [EMBOSS] question about PRINTS Message-ID: <20050518163556.GA28052@bigben.ulb.ac.be> Dear colleagues, I have a question about the PRINTS database (needed for the program pscan). I have noticed that there have been no updates since already almost 2 years. Did they give up the maintenance ? Does someone know more about this ? Guy Bottu, BEN From rls at ebi.ac.uk Wed May 18 14:48:00 2005 From: rls at ebi.ac.uk (Rodrigo Lopez) Date: Wed, 18 May 2005 19:48:00 +0100 Subject: [EMBOSS] question about PRINTS In-Reply-To: <20050518163556.GA28052@bigben.ulb.ac.be> Message-ID: <001601c55bda$1ebb80d0$0fd81452@castafiore> You should contact Terry Attwood (attwood at bioinf.man.ac.uk) about PRINTS. R:) > -----Original Message----- > From: owner-emboss at hgmp.mrc.ac.uk > [mailto:owner-emboss at hgmp.mrc.ac.uk] On Behalf Of Guy Bottu > Sent: 18 May 2005 17:36 > To: emboss at embnet.org > Subject: [EMBOSS] question about PRINTS > > > Dear colleagues, > > I have a question about the PRINTS database (needed for the program > pscan). I have noticed that there have been no updates since already > almost 2 years. Did they give up the maintenance ? Does > someone know more > about this ? > > Guy Bottu, > BEN > From isabelle.wells at roche.com Thu May 19 11:12:00 2005 From: isabelle.wells at roche.com (Wells, Isabelle) Date: Thu, 19 May 2005 17:12:00 +0200 Subject: [EMBOSS] Help with retrieving the indexing date Message-ID: <062896243F02D445AB77BD2B51E2F3738898B1@rbamsem3.emea.roche.com> Hello all, I am using dbiflat to index our databases with the option -date dd/mm/yy. It seems this date should be stored in the binary index files. Is there a way or a tool to extract this date from the file? Thanks for your help, > Isabelle > +--- O---O ------------------------------------------- o-o Isabelle Wells, Ph. D. O F. Hoffmann-La Roche Ltd o-o Bioinformatics o---o PRBI-P, building 65/307 o----o CH-4070 Basel, Switzerland O----O 0--o O o-o E-mail: isabelle.wells at roche.com +- o---o --------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20050519/719a065e/attachment.html From pmr at ebi.ac.uk Thu May 19 11:37:06 2005 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Thu, 19 May 2005 16:37:06 +0100 (BST) Subject: [EMBOSS] Help with retrieving the indexing date In-Reply-To: <062896243F02D445AB77BD2B51E2F3738898B1@rbamsem3.emea.roche.com> References: <062896243F02D445AB77BD2B51E2F3738898B1@rbamsem3.emea.roche.com> Message-ID: <1647.128.211.168.136.1116517026.squirrel@webmail.ebi.ac.uk> Hi Isabelle, > I am using dbiflat to index our databases with the option -date > dd/mm/yy. It seems this date should be stored in the binary index files. > Is there a way or a tool to extract this date from the file? > Thanks for your help, There is a script that is included in the scripts directory for debugging. I would like to extract information such as the index data when retrieving sequences and in showdb, but it is complicated because only the EMBLCD databases (index by dbiflat and the other dbi tools in EMBOSS) have the date easily available. We could, perhaps, try to get the date for SRS and SRSWWW and SRSFASTA databases. We could also look into retrieving dates from the new indexing system under development to replace EMBLCD (and dbiflat). How useful would this be? Perhaps as an extra option to showdb, because it will be slow to retrieve the information from a lareg number of external databases. Hope this helps, Peter Rice From isabelle.wells at roche.com Fri May 20 04:39:21 2005 From: isabelle.wells at roche.com (Wells, Isabelle) Date: Fri, 20 May 2005 10:39:21 +0200 Subject: [EMBOSS] Help with retrieving the indexing date Message-ID: <062896243F02D445AB77BD2B51E2F3738AE8EF@rbamsem3.emea.roche.com> Hi Peter, Thanks very much for the info. We found the script and were able to write a program which reads this date. We don't have SRS databases but an extra option in showdb to show the date would have been useful. Best regards, Isabelle -----Original Message----- From: pmr at ebi.ac.uk [mailto:pmr at ebi.ac.uk] Sent: Thursday, May 19, 2005 17:37 To: Wells, Isabelle {PRBI~Basel} Cc: emboss at embnet.org Subject: Re: [EMBOSS] Help with retrieving the indexing date Hi Isabelle, > I am using dbiflat to index our databases with the option -date > dd/mm/yy. It seems this date should be stored in the binary index > files. Is there a way or a tool to extract this date from the file? > Thanks for your help, There is a script that is included in the scripts directory for debugging. I would like to extract information such as the index data when retrieving sequences and in showdb, but it is complicated because only the EMBLCD databases (index by dbiflat and the other dbi tools in EMBOSS) have the date easily available. We could, perhaps, try to get the date for SRS and SRSWWW and SRSFASTA databases. We could also look into retrieving dates from the new indexing system under development to replace EMBLCD (and dbiflat). How useful would this be? Perhaps as an extra option to showdb, because it will be slow to retrieve the information from a lareg number of external databases. Hope this helps, Peter Rice From atorrano at lsi.upc.edu Fri May 20 06:52:33 2005 From: atorrano at lsi.upc.edu (Alexis Torrano Martinez) Date: Fri, 20 May 2005 12:52:33 +0200 (MET DST) Subject: [EMBOSS] seqret Message-ID: <7462737191atorrano@lsi.upc.es> Hello. I have just begun to use emboss. I'd like to ask some question. Let the next tuple be my DB descriptor : DB myDB [ dir: /..../myDBdir indexdirectory: /..../indexesForMyDB ] Is it possible to split the DB through different directories or disks? On two 300Gb disks mounted on /mnt/d1 and /mnt/d2, I put some files on d1 and the other on d2... so, a tuple like the next, would it be correct? DB myDB [ dir: /mnt/d1/myDB dir: /mnt/d2/myDB indexdirectory: /..../indexesForMyDB ] or DB myDB [ dir: /mnt/d1/myDB : /mnt/d2/myDB indexdirectory: /..../indexesForMyDB ] How would be done such split?? A lot of thanks, and best regards. Alexis. From jison at hgmp.mrc.ac.uk Fri May 20 07:15:33 2005 From: jison at hgmp.mrc.ac.uk (Dr J.C. Ison) Date: Fri, 20 May 2005 12:15:33 +0100 Subject: [EMBOSS] seqret References: <7462737191atorrano@lsi.upc.es> Message-ID: <428DC6D5.97F40476@hgmp.mrc.ac.uk> Dear Alexis So far as I am aware it is not possible to split a database in that way. You would need two separate definitions for the different parts (d1/myDB and d2/myDB). Cheers Jon Alexis Torrano Martinez wrote: > > Hello. > > I have just begun to use emboss. I'd like to ask some question. > Let the next tuple be my DB descriptor : > > DB myDB [ > > dir: /..../myDBdir > indexdirectory: /..../indexesForMyDB > ] > > Is it possible to split the DB through different directories or disks? > On two 300Gb disks mounted on /mnt/d1 and /mnt/d2, I put some files on > d1 and the other on d2... so, a tuple like the next, would it be correct? > > DB myDB [ > > dir: /mnt/d1/myDB > dir: /mnt/d2/myDB > indexdirectory: /..../indexesForMyDB > ] > > or > > DB myDB [ > > dir: /mnt/d1/myDB : /mnt/d2/myDB > indexdirectory: /..../indexesForMyDB > ] > > How would be done such split?? > > A lot of thanks, and best regards. > > Alexis. -- Jon C. Ison, PhD Proteomics Applications Group MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK Tel: +44 1223 494500 Fax: +44 1223 494512 E-mail: jison at rfcgr.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk From pmr at ebi.ac.uk Fri May 20 07:39:10 2005 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Fri, 20 May 2005 12:39:10 +0100 (BST) Subject: [EMBOSS] seqret In-Reply-To: <7462737191atorrano@lsi.upc.es> References: <7462737191atorrano@lsi.upc.es> Message-ID: <1288.128.210.190.180.1116589150.squirrel@webmail.ebi.ac.uk> Dear Alexis, > Is it possible to split the DB through different directories or disks? > On two 300Gb disks mounted on /mnt/d1 and /mnt/d2, I put some files on > d1 and the other on d2... so, a tuple like the next, would it be correct? > > How would be done such split?? The indexing format we use in EMBOSS was developed for the Staden package some years ago, and has no space to store more than one directory. 1. use symbolic links - either add links to /mnt/d1 that point to the files in /mnt/d2, or create a new directory /mnt/d0 with symlinks to all the files in /mnt/d1 and /mnt/d2 2. we are working on a new indexing system where we may be able to allow multiple directories, but it does add extra complexity. We will look into the possibility. Hope that helps, regards, Peter Rice From leongmz at gmail.com Sat May 21 03:41:19 2005 From: leongmz at gmail.com (Michael Leong) Date: Sat, 21 May 2005 00:41:19 -0700 Subject: [EMBOSS] Jemboss launch killing cpu Message-ID: <6.1.2.0.2.20050521003703.02f8d6d8@ifurita.dyndns.org> Hi. I'm trying to setup Jemboss on my lan and trying to use the java webstart to launch it. However, on the Jemboss login window, when the progress meter reaches about 50%, it locks up and eats all teh cpu. Thx, mike Here are the steps at I took to install it: #------------------------------------------------------ untar EMBOSSS 2.10.0 untar tomcat 5.5.9 download emboss install script for tomcat 5.5.x untar axis 1.2 mkdir /opt/emboss-data/soap chmod 777 /opt/emboss-data/soap chmod a+t /opt/emboss-data/soap replace install script w/ one for tomcat 5.5.x run ./install-jemboss-server.sh install options: client-server os: linux ip: 192.168.2.108 ssl: yes port: 8443 java: jdk v1.5 unix auth: yes tomcat uid: 1000 auth method: shadow embassy pkgs: no clustalw: /usr/bin primer3_core: auto deploy: yes modifed server.xml as told got warning about javax.activation.DataHandler and javax.mail.internet.MimeMultipart not found chown root /opt/emboss/bin/jembossctl chmod u+s /opt/emboss/bin/jembossctl cd /opt/emboss/share/EMBOSS/jemboss/utils ./makeJNLP.sh edit /opt/emboss/share/EMBOSS/jemboss/jnlp/index.html and Jemboss.jnlp to proper webserver copy /opt/emboss/share/EMBOSS/jemboss/jnlp/* to webserver #------------------------------------------------------ From ableasby at hgmp.mrc.ac.uk Sat May 21 04:26:00 2005 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Sat, 21 May 2005 09:26:00 +0100 (BST) Subject: [EMBOSS] Jemboss launch killing cpu Message-ID: <200505210826.j4L8Q0UB014121@bromine.hgmp.mrc.ac.uk> Dear Mike, The first thing to check with those symptoms is that you are running JDK 5.0 Update 3. Previous versions of java 1.5 under linux had a JWS bug which caused such a CPU-eating problem. HTH Alan Bleasby HGMP/RFCGR (for a little while) From leongmz at gmail.com Sat May 21 05:01:21 2005 From: leongmz at gmail.com (Michael Leong) Date: Sat, 21 May 2005 02:01:21 -0700 Subject: [EMBOSS] Jemboss launch killing cpu In-Reply-To: <200505210826.j4L8Q0UB014121@bromine.hgmp.mrc.ac.uk> References: <200505210826.j4L8Q0UB014121@bromine.hgmp.mrc.ac.uk> Message-ID: <6.1.2.0.2.20050521015918.02f790c8@pop.gmail.com> Still same problem after I upgarded. server: linux 2.4.27-om-20040808, jdk 1.50, update3 client : windows 2000, jre 1.50, updatae 3 At 01:26 AM 5/21/2005, Alan Bleasby wrote: >Dear Mike, > >The first thing to check with those symptoms is that you >are running JDK 5.0 Update 3. Previous versions of java 1.5 >under linux had a JWS bug which caused such a CPU-eating >problem. > >HTH > >Alan Bleasby >HGMP/RFCGR (for a little while) From leongmz at gmail.com Sat May 21 06:05:36 2005 From: leongmz at gmail.com (Michael Leong) Date: Sat, 21 May 2005 03:05:36 -0700 Subject: [EMBOSS] Jemboss launch killing cpu In-Reply-To: <200505210923.j4L9NGO7006557@bromine.hgmp.mrc.ac.uk> References: <200505210923.j4L9NGO7006557@bromine.hgmp.mrc.ac.uk> Message-ID: <6.1.2.0.2.20050521030142.02ebe478@pop.gmail.com> Grr.. this is bad. Every jre/os combination drained the cpu. w2k/jre 1.5, update 2 w2k/jre 1.5, update 3 w2k/jre 1.4.2 update 8 linux/jre 1.5, update 3 Are there another gui cflient equalivent to jemboss (functionality, support, etc) thx, mike At 02:23 AM 5/21/2005, Alan Bleasby wrote: >Dear Mike, > >The JWS bug would have affected a linux client but yours looks >to be a windows one. I assume the CPU-eating is happening on >the client? > >I'm CCing this to Tim Carver (jemboss author) who, I believe, >gets back from holiday this weekend. He may be able to help. > >Alan Bleasby > > >Hi. > >I'm trying to setup Jemboss on my lan and trying to use the java webstart >to launch it. However, on the Jemboss login window, when the progress >meter reaches about 50%, it locks up and eats all teh cpu. > >Thx, >mike > >Here are the steps at I took to install it: > >#------------------------------------------------------ >untar EMBOSSS 2.10.0 >untar tomcat 5.5.9 >download emboss install script for tomcat 5.5.x >untar axis 1.2 >mkdir /opt/emboss-data/soap >chmod 777 /opt/emboss-data/soap >chmod a+t /opt/emboss-data/soap > >replace install script w/ one for tomcat 5.5.x >run ./install-jemboss-server.sh > >install options: >client-server >os: linux >ip: 192.168.2.108 >ssl: yes >port: 8443 >java: jdk v1.5 >unix auth: yes >tomcat uid: 1000 >auth method: shadow >embassy pkgs: no >clustalw: /usr/bin >primer3_core: >auto deploy: yes >modifed server.xml as told >got warning about javax.activation.DataHandler and >javax.mail.internet.MimeMultipart not found > > chown root /opt/emboss/bin/jembossctl > chmod u+s /opt/emboss/bin/jembossctl > >cd /opt/emboss/share/EMBOSS/jemboss/utils >./makeJNLP.sh > >edit /opt/emboss/share/EMBOSS/jemboss/jnlp/index.html and Jemboss.jnlp to >proper webserver > >copy /opt/emboss/share/EMBOSS/jemboss/jnlp/* to webserver >#------------------------------------------------------ From ableasby at hgmp.mrc.ac.uk Sat May 21 06:49:14 2005 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Sat, 21 May 2005 11:49:14 +0100 (BST) Subject: [EMBOSS] Jemboss launch killing cpu Message-ID: <200505211049.j4LAnE8m010022@bromine.hgmp.mrc.ac.uk> >Are there another gui cflient equalivent to jemboss No, all interfaces have their different strengths and weaknesses. For other interfaces see: http://emboss.sourceforge.net/interfaces/#interfaces We will be doing an in depth GUI survey in the near future. [oh, and I'd appreciate it if email I sent to you off-list was not posted back to the list. Thanks] HTH Alan Bleasby HGMP/RFCGR From leongmz at gmail.com Sat May 21 15:26:56 2005 From: leongmz at gmail.com (Michael Leong) Date: Sat, 21 May 2005 12:26:56 -0700 Subject: [EMBOSS] Jemboss launch killing cpu In-Reply-To: <200505211049.j4LAnE8m010022@bromine.hgmp.mrc.ac.uk> References: <200505211049.j4LAnE8m010022@bromine.hgmp.mrc.ac.uk> Message-ID: <6.1.2.0.2.20050521122601.02eca198@pop.gmail.com> At 03:49 AM 5/21/2005, Alan Bleasby wrote: > >Are there another gui cflient equalivent to jemboss > >No, all interfaces have their different strengths and weaknesses. >For other interfaces see: > http://emboss.sourceforge.net/interfaces/#interfaces > >We will be doing an in depth GUI survey in the near future. > >[oh, and I'd appreciate it if email I sent to you off-list was not > posted back to the list. Thanks] my apologies. mike >HTH > >Alan Bleasby >HGMP/RFCGR From leongmz at gmail.com Sun May 22 16:02:04 2005 From: leongmz at gmail.com (Michael Leong) Date: Sun, 22 May 2005 13:02:04 -0700 Subject: [EMBOSS] Jemboss Login problem Message-ID: <6.1.2.0.2.20050522125831.02f4ef40@ifurita.dyndns.org> Hi, I got Jemboss running on my lan, but it keep saying my login is incorrect. I've used the install-jemboss-server.sh script to install the entire pkg. auth method is linux/shadow. The tomcat user has permission to read /etc/shadow. setting: java: 1.4.2_8 tomcat: 5.0.30 axis: 1.1 emboss: 2.9.0 w/ the Jemboss patches. os: linux auth: shadow thx, mike From leongmz at gmail.com Sun May 22 18:30:10 2005 From: leongmz at gmail.com (Michael Leong) Date: Sun, 22 May 2005 15:30:10 -0700 Subject: [EMBOSS] Jemboss Login problem In-Reply-To: <6.1.2.0.2.20050522125831.02f4ef40@ifurita.dyndns.org> References: <6.1.2.0.2.20050522125831.02f4ef40@ifurita.dyndns.org> Message-ID: <6.1.2.0.2.20050522145328.02f226b8@pop.gmail.com> Got the following error on jemboss_error.log w/ shadow: Failed Authorisation mike STDERR java_pipe_read timeout java_rcv error Pipe Recv error 1 with pam: Failed Authorisation mike STDERR Other than that, can't find any thing else on At 01:02 PM 5/22/2005, Michael Leong wrote: >Hi, > >I got Jemboss running on my lan, but it keep saying my login is incorrect. > >I've used the install-jemboss-server.sh script to install the entire pkg. > >auth method is linux/shadow. The tomcat user has permission to read >/etc/shadow. > > >setting: >java: 1.4.2_8 >tomcat: 5.0.30 >axis: 1.1 >emboss: 2.9.0 w/ the Jemboss patches. >os: linux >auth: shadow > > >thx, > >mike > From asonyadi at cp.co.id Sun May 22 20:55:43 2005 From: asonyadi at cp.co.id (Sony Adi Susanto) Date: Mon, 23 May 2005 07:55:43 +0700 Subject: [EMBOSS] please unsubscribe Message-ID: Biotechnology Department Research & Development Center, PT Charoen Pokphand Indonesia Tbk Jl. Parangtritis Raya Blok A-5E No.12A Ancol Barat, Jakarta, DKI Jakarta Indonesia Telp : 62-251-6926241 Fax : 62-351-6930364 Email address : asonyadi at cp.co.id; asonyadi at yahoo.com.sg -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20050523/9b72d378/attachment.html From jeremy at biochem.uthscsa.edu Wed May 25 11:59:19 2005 From: jeremy at biochem.uthscsa.edu (Jeremy Mann) Date: Wed, 25 May 2005 10:59:19 -0500 (CDT) Subject: [EMBOSS] Installation help Message-ID: <46609.129.111.174.49.1117036759.squirrel@biochem.uthscsa.edu> I am having a very difficult time getting the EMBOSS client/server install on a Suse Linux 9.1 system. I have followed the instructions precisely. Tomcat starts, then gives me this error. Note I have also tried this with the newer 5.5.9 Tomcat (with new install file) and this still happens: Please wait, starting tomcat....... Using CATALINA_BASE: /usr/local/jakarta-tomcat-5.0.30 Using CATALINA_HOME: /usr/local/jakarta-tomcat-5.0.30 Using CATALINA_TMPDIR: /usr/local/jakarta-tomcat-5.0.30/temp Using JAVA_HOME: /usr/lib/java May 25, 2005 10:27:53 AM org.apache.axis.utils.JavaUtils isAttachmentSupported WARNING: Unable to find required classes (javax.activation.DataHandler and javax.mail.internet.MimeMultipart). Attachment support is disabled. Processing file JembossServer.wsdd Exception: AxisFault faultCode: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException faultSubcode: faultString: java.net.ConnectException: Connection refused faultActor: faultNode: faultDetail: {http://xml.apache.org/axis/}stackTrace:java.net.ConnectException: Connection refused at java.net.PlainSocketImpl.socketConnect(Native Method) at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:305) at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:171) at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:158) at java.net.Socket.connect(Socket.java:452) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:324) at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFactory.java:135) at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFactory.java:99) at org.apache.axis.transport.http.HTTPSender.getSocket(HTTPSender.java:130) at org.apache.axis.transport.http.HTTPSender.writeToSocket(HTTPSender.java:382) at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:88) at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32) at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118) at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83) at org.apache.axis.client.AxisClient.invoke(AxisClient.java:147) at org.apache.axis.client.Call.invokeEngine(Call.java:2737) at org.apache.axis.client.Call.invoke(Call.java:2720) at org.apache.axis.client.Call.invoke(Call.java:1756) at org.apache.axis.client.AdminClient.process(AdminClient.java:438) at org.apache.axis.client.AdminClient.process(AdminClient.java:403) at org.apache.axis.client.AdminClient.process(AdminClient.java:409) at org.apache.axis.client.AdminClient.process(AdminClient.java:319) at org.apache.axis.client.AdminClient.main(AdminClient.java:462) {http://xml.apache.org/axis/}hostname:bcf Tomcat is active on port 8080, even though I told the install script to use 8443. Also, there is no Axis service for emboss, only version and admin. What is going wrong with my installation? -- 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 robin at hms.harvard.edu Wed May 25 13:33:50 2005 From: robin at hms.harvard.edu (Robin Colgrove) Date: Wed, 25 May 2005 13:33:50 -0400 Subject: [EMBOSS] Installation help In-Reply-To: <46609.129.111.174.49.1117036759.squirrel@biochem.uthscsa.edu> References: <46609.129.111.174.49.1117036759.squirrel@biochem.uthscsa.edu> Message-ID: <70a549240c9938139675c7c16231a0b6@hms.harvard.edu> Hello all, After numerous attempts following suggestions on this list, I never have been able to get the X11 version of EMBOSS to install on my iBook under Mac OS X 10.3.8, but I installed and have been using the command line version without trouble (and using the GUI programs remotely with EMBOSS on a server and running the Mac X11 client locally). Next week I am going to upgrade to OSX 10.4 "Tiger", and was thinking of trying a full EMBOSS install again. I would be interested to hear from anyone who has done this (EMBOSS on Tiger) and any tips/advice. Also, it is not clear to me whether it would be best to uninstall everything and reinstall, or whether I could just install the X11 parts over an existing install. thanks Robin Colgrove Dept of Microbiology Harvard Medical School From leongmz at gmail.com Wed May 25 14:06:47 2005 From: leongmz at gmail.com (Michael Leong) Date: Wed, 25 May 2005 11:06:47 -0700 Subject: [EMBOSS] Installation help In-Reply-To: <46609.129.111.174.49.1117036759.squirrel@biochem.uthscsa.e du> References: <46609.129.111.174.49.1117036759.squirrel@biochem.uthscsa.edu> Message-ID: <6.1.2.0.2.20050525110553.02dd03d0@pop.gmail.com> If you're using tomcat 5.5.9, get the newer install-jemboss-server.sh script from the website. mike At 08:59 AM 5/25/2005, Jeremy Mann wrote: >I am having a very difficult time getting the EMBOSS client/server install >on a Suse Linux 9.1 system. I have followed the instructions precisely. >Tomcat starts, then gives me this error. Note I have also tried this with >the newer 5.5.9 Tomcat (with new install file) and this still happens: > >Please wait, starting tomcat....... >Using CATALINA_BASE: /usr/local/jakarta-tomcat-5.0.30 >Using CATALINA_HOME: /usr/local/jakarta-tomcat-5.0.30 >Using CATALINA_TMPDIR: /usr/local/jakarta-tomcat-5.0.30/temp >Using JAVA_HOME: /usr/lib/java > > >May 25, 2005 10:27:53 AM org.apache.axis.utils.JavaUtils >isAttachmentSupported >WARNING: Unable to find required classes (javax.activation.DataHandler and >javax.mail.internet.MimeMultipart). Attachment support is disabled. >Processing file JembossServer.wsdd >Exception: AxisFault > faultCode: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException > faultSubcode: > faultString: java.net.ConnectException: Connection refused > faultActor: > faultNode: > faultDetail: > {http://xml.apache.org/axis/}stackTrace:java.net.ConnectException: >Connection refused > at java.net.PlainSocketImpl.socketConnect(Native Method) > at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:305) > at >java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:171) > at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:158) > at java.net.Socket.connect(Socket.java:452) > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at >sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) > at >sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) > at java.lang.reflect.Method.invoke(Method.java:324) > at >org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFactory.java:135) > at >org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFactory.java:99) > at >org.apache.axis.transport.http.HTTPSender.getSocket(HTTPSender.java:130) > at >org.apache.axis.transport.http.HTTPSender.writeToSocket(HTTPSender.java:382) > at >org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:88) > at >org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32) > at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118) > at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83) > at org.apache.axis.client.AxisClient.invoke(AxisClient.java:147) > at org.apache.axis.client.Call.invokeEngine(Call.java:2737) > at org.apache.axis.client.Call.invoke(Call.java:2720) > at org.apache.axis.client.Call.invoke(Call.java:1756) > at org.apache.axis.client.AdminClient.process(AdminClient.java:438) > at org.apache.axis.client.AdminClient.process(AdminClient.java:403) > at org.apache.axis.client.AdminClient.process(AdminClient.java:409) > at org.apache.axis.client.AdminClient.process(AdminClient.java:319) > at org.apache.axis.client.AdminClient.main(AdminClient.java:462) > > {http://xml.apache.org/axis/}hostname:bcf > >Tomcat is active on port 8080, even though I told the install script to >use 8443. Also, there is no Axis service for emboss, only version and >admin. > >What is going wrong with my installation? > > > > >-- >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 jeremy at biochem.uthscsa.edu Wed May 25 14:31:12 2005 From: jeremy at biochem.uthscsa.edu (Jeremy Mann) Date: Wed, 25 May 2005 13:31:12 -0500 (CDT) Subject: [EMBOSS] Installation help In-Reply-To: References: <46609.129.111.174.49.1117036759.squirrel@biochem.uthscsa.edu> Message-ID: <50678.129.111.174.49.1117045872.squirrel@biochem.uthscsa.edu> Tim Carver said: > Hi Jeremy > > If tomcat is not using 8443 then the deployment of the Jemboss services > will fail. When you run the script you are asked to cut and paste lines > into conf/server.xml. Did you do this? Are there any error in the tomcat > logs/catalina.out. > > Btw, running the script from scratch will mean that you need a fresh copy > of tomcat, EMBOSS and axis and you will need to remove the previous EMBOSS > installation directories. I just tried again for the 6th time. Yes, I copy pasted the lines to the bottom of server.xml. Catalina.out: Created MBeanServer with ID: 147c5fc:104151818da:-8000:bcf:1 May 25, 2005 1:23:18 PM org.apache.tomcat.util.digester.Digester fatalError SEVERE: Parse Fatal Error at line 380 column 6: The markup in the document following the root element must be well-formed. org.xml.sax.SAXParseException: The markup in the document following the root element must be well-formed. at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source) at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source) at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source) at org.apache.xerces.impl.XMLDocumentScannerImpl$TrailingMiscDispatcher.dispatch(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) at org.apache.tomcat.util.digester.Digester.parse(Digester.java:1561) at org.apache.catalina.startup.Catalina.load(Catalina.java:473) at org.apache.catalina.startup.Catalina.load(Catalina.java:509) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:324) at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:243) at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:408) May 25, 2005 1:23:18 PM org.apache.catalina.startup.Catalina load WARNING: Catalina.start using conf/server.xml: org.xml.sax.SAXParseException: The markup in the document following the root element must be well-formed. at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) at org.apache.tomcat.util.digester.Digester.parse(Digester.java:1561) at org.apache.catalina.startup.Catalina.load(Catalina.java:473) at org.apache.catalina.startup.Catalina.load(Catalina.java:509) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:324) at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:243) at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:408) May 25, 2005 1:23:18 PM org.apache.coyote.http11.Http11Protocol init INFO: Initializing Coyote HTTP/1.1 on http-8080 May 25, 2005 1:23:18 PM org.apache.catalina.core.StandardService start INFO: Starting service Catalina May 25, 2005 1:23:18 PM org.apache.catalina.core.StandardEngine start INFO: Starting Servlet Engine: Apache Tomcat/5.5.9 May 25, 2005 1:23:18 PM org.apache.catalina.core.StandardHost start INFO: XML validation disabled - Unable to find config file. Creating new servlet engine config file: /WEB-INF/server-config.wsdd May 25, 2005 1:23:21 PM org.apache.coyote.http11.Http11Protocol start INFO: Starting Coyote HTTP/1.1 on http-8080 May 25, 2005 1:23:21 PM org.apache.jk.common.ChannelSocket init INFO: JK: ajp13 listening on /0.0.0.0:8009 May 25, 2005 1:23:21 PM org.apache.jk.server.JkMain start INFO: Jk running ID=0 time=0/31 config=null May 25, 2005 1:23:21 PM org.apache.catalina.storeconfig.StoreLoader load INFO: Find registry server-registry.xml at classpath resource May 25, 2005 1:23:21 PM org.apache.catalina.startup.Catalina start INFO: Server startup in 3219 ms Install script: Please wait, starting tomcat....... Using CATALINA_BASE: /usr/local/jakarta-tomcat-5.5.9 Using CATALINA_HOME: /usr/local/jakarta-tomcat-5.5.9 Using CATALINA_TMPDIR: /usr/local/jakarta-tomcat-5.5.9/temp Using JRE_HOME: /usr/lib/java/jre May 25, 2005 1:19:08 PM org.apache.axis.utils.JavaUtils isAttachmentSupported WARNING: Unable to find required classes (javax.activation.DataHandler and javax.mail.internet.MimeMultipart). Attachment support is disabled. Processing file JembossServer.wsdd Exception: AxisFault faultCode: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException faultSubcode: faultString: java.net.ConnectException: Connection refused faultActor: faultNode: faultDetail: {http://xml.apache.org/axis/}stackTrace:java.net.ConnectException: Connection refused at java.net.PlainSocketImpl.socketConnect(Native Method) at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:305) at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:171) at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:158) at java.net.Socket.connect(Socket.java:452) at com.sun.net.ssl.internal.ssl.SSLSocketImpl.connect(DashoA12275) at com.sun.net.ssl.internal.ssl.SSLSocketImpl.<init>(DashoA12275) at com.sun.net.ssl.internal.ssl.SSLSocketFactoryImpl.createSocket(DashoA12275) at org.apache.axis.components.net.JSSESocketFactory.create(JSSESocketFactory.java:92) at org.apache.axis.transport.http.HTTPSender.getSocket(HTTPSender.java:130) at org.apache.axis.transport.http.HTTPSender.writeToSocket(HTTPSender.java:382) at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:88) at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32) at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118) at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83) at org.apache.axis.client.AxisClient.invoke(AxisClient.java:147) at org.apache.axis.client.Call.invokeEngine(Call.java:2737) at org.apache.axis.client.Call.invoke(Call.java:2720) at org.apache.axis.client.Call.invoke(Call.java:1756) at org.apache.axis.client.AdminClient.process(AdminClient.java:438) at org.apache.axis.client.AdminClient.process(AdminClient.java:403) at org.apache.axis.client.AdminClient.process(AdminClient.java:409) at org.apache.axis.client.AdminClient.process(AdminClient.java:319) at org.apache.axis.client.AdminClient.main(AdminClient.java:462) {http://xml.apache.org/axis/}hostname:bcf -- 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 kvddrift at earthlink.net Wed May 25 18:20:22 2005 From: kvddrift at earthlink.net (Koen van der Drift) Date: Wed, 25 May 2005 18:20:22 -0400 Subject: [EMBOSS] Installation help In-Reply-To: <70a549240c9938139675c7c16231a0b6@hms.harvard.edu> References: <46609.129.111.174.49.1117036759.squirrel@biochem.uthscsa.edu> <70a549240c9938139675c7c16231a0b6@hms.harvard.edu> Message-ID: <870f792bbfbc294665000e811f692f44@earthlink.net> Hi Robin, Which X11 GUI are you trying to use? I have no experience yet with Tiger, but have no problems with using the kaptain GUI (installed through fink). - Koen. On May 25, 2005, at 1:33 PM, Robin Colgrove wrote: > > Hello all, > > After numerous attempts following suggestions on this list, I never > have been able to get the X11 version of EMBOSS to install on my iBook > under Mac OS X 10.3.8, but I installed and have been using the command > line version without trouble (and using the GUI programs remotely with > EMBOSS on a server and running the Mac X11 client locally). > > Next week I am going to upgrade to OSX 10.4 "Tiger", and was thinking > of trying a full EMBOSS install again. I would be interested to hear > from anyone who has done this (EMBOSS on Tiger) and any tips/advice. > Also, it is not clear to me whether it would be best to uninstall > everything and reinstall, or whether I could just install the X11 > parts over an existing install. > > thanks > > Robin Colgrove > Dept of Microbiology > Harvard Medical School > From mbb8n at virginia.edu Wed May 25 19:47:22 2005 From: mbb8n at virginia.edu (Michael Black) Date: Wed, 25 May 2005 19:47:22 -0400 Subject: [EMBOSS] Installation help In-Reply-To: <70a549240c9938139675c7c16231a0b6@hms.harvard.edu> References: <46609.129.111.174.49.1117036759.squirrel@biochem.uthscsa.edu> <70a549240c9938139675c7c16231a0b6@hms.harvard.edu> Message-ID: <3502496E-6BAC-4571-B012-A00F8BE16D74@virginia.edu> Robin, are you referring to the JemBoss installation? And do you mean a standalone installation, or a server installation? I've never had a problem installing Jemboss/EMBOSS (and the Embassy packages) standalone in Jaguar, Panther and now Tiger. PNG support requires some additional efforts (FINK takes care of that, for me). Jemboss 1.5 and EMBOSS 2.10.0 run fine on my powerbook under Tiger. I always run the jemboos installer script to install everything (embassy included), and follow the Jemboss installation guide for OS X. I also have it running fine on a dual-2.5GHz G5 running Panther 10.3.9. When you update to Tiger, be sure to check the install option for the new X11, and then, install the developers tools and the new X11 SDK. And with Tiger, do NOT point the jemboss install script to Java 1.5, stick with 1.4.2, or even 1.3. Michael ____________________________________________ Michael B. Black, Ph.D. Molecular Biology Computing Support ITC-ACHS, MSB rm.3013 982-4039 mblack at virginia.edu Web support, see the Molecular Biology section at: http://www.itc.virginia.edu/achs ____________________________________________ On May 25, 2005, at 1:33 PM, Robin Colgrove wrote: > > Hello all, > > After numerous attempts following suggestions on this list, I never > have been able to get the X11 version of EMBOSS to install on my > iBook under Mac OS X 10.3.8, but I installed and have been using > the command line version without trouble (and using the GUI > programs remotely with EMBOSS on a server and running the Mac X11 > client locally). > > Next week I am going to upgrade to OSX 10.4 "Tiger", and was > thinking of trying a full EMBOSS install again. I would be > interested to hear from anyone who has done this (EMBOSS on Tiger) > and any tips/advice. Also, it is not clear to me whether it would > be best to uninstall everything and reinstall, or whether I could > just install the X11 parts over an existing install. > > thanks > > Robin Colgrove > Dept of Microbiology > Harvard Medical School > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20050525/007800c9/attachment.html From tjc at sanger.ac.uk Thu May 26 05:58:28 2005 From: tjc at sanger.ac.uk (Tim Carver) Date: Thu, 26 May 2005 10:58:28 +0100 (BST) Subject: [EMBOSS] Installation help (fwd) Message-ID: Thanks Michael that is useful to the EMBOSS group as we are waiting for a copy of Tiger to test Jemboss/EMBOSS out on. So it is good to know that you have it working. Also just a note that 1.3 is no longer supported, so the options are 1.4.2 or 1.5. Regards Tim Carver On Wed, 25 May 2005, Michael Black wrote: > Robin, are you referring to the JemBoss installation? And do you > mean a standalone installation, or a server installation? > > I've never had a problem installing Jemboss/EMBOSS (and the Embassy > packages) standalone in Jaguar, Panther and now Tiger. PNG support > requires some additional efforts (FINK takes care of that, for me). > Jemboss 1.5 and EMBOSS 2.10.0 run fine on my powerbook under Tiger. > > I always run the jemboos installer script to install everything > (embassy included), and follow the Jemboss installation guide for OS > X. I also have it running fine on a dual-2.5GHz G5 running Panther > 10.3.9. > > When you update to Tiger, be sure to check the install option for the > new X11, and then, install the developers tools and the new X11 SDK. > And with Tiger, do NOT point the jemboss install script to Java 1.5, > stick with 1.4.2, or even 1.3. > > Michael > ____________________________________________ > Michael B. Black, Ph.D. > Molecular Biology Computing Support > ITC-ACHS, MSB rm.3013 > 982-4039 > mblack at virginia.edu > > Web support, see the Molecular Biology > section at: http://www.itc.virginia.edu/achs > ____________________________________________ > > > > On May 25, 2005, at 1:33 PM, Robin Colgrove wrote: > > > > > Hello all, > > > > After numerous attempts following suggestions on this list, I never > > have been able to get the X11 version of EMBOSS to install on my > > iBook under Mac OS X 10.3.8, but I installed and have been using > > the command line version without trouble (and using the GUI > > programs remotely with EMBOSS on a server and running the Mac X11 > > client locally). > > > > Next week I am going to upgrade to OSX 10.4 "Tiger", and was > > thinking of trying a full EMBOSS install again. I would be > > interested to hear from anyone who has done this (EMBOSS on Tiger) > > and any tips/advice. Also, it is not clear to me whether it would > > be best to uninstall everything and reinstall, or whether I could > > just install the X11 parts over an existing install. > > > > thanks > > > > Robin Colgrove > > Dept of Microbiology > > Harvard Medical School > > > > > > The Wellcome Trust Sanger Institute Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK From kvddrift at earthlink.net Thu May 26 06:32:24 2005 From: kvddrift at earthlink.net (Koen van der Drift) Date: Thu, 26 May 2005 06:32:24 -0400 Subject: [EMBOSS] Installation help In-Reply-To: <3502496E-6BAC-4571-B012-A00F8BE16D74@virginia.edu> References: <46609.129.111.174.49.1117036759.squirrel@biochem.uthscsa.edu> <70a549240c9938139675c7c16231a0b6@hms.harvard.edu> <3502496E-6BAC-4571-B012-A00F8BE16D74@virginia.edu> Message-ID: On May 25, 2005, at 7:47 PM, Michael Black wrote: > When you update to Tiger, be sure to check the install option for the > new X11, and then, install the developers tools and the new X11 SDK.? > And with Tiger, do NOT point the jemboss install script to Java 1.5, > stick with 1.4.2, or even 1.3. > Michael, What is the complete path to 1.4.2 on Tiger (on 10.3 it is "/System/Library/Frameworks/JavaVM.framework/Versions/1.4.2") ? I am the maintainer of the emboss package for fink and want to make sure that 1.5 is not used. thanks, - Koen. From mbb8n at virginia.edu Thu May 26 08:00:46 2005 From: mbb8n at virginia.edu (Michael Black) Date: Thu, 26 May 2005 08:00:46 -0400 Subject: [EMBOSS] Installation help In-Reply-To: References: <46609.129.111.174.49.1117036759.squirrel@biochem.uthscsa.edu> <70a549240c9938139675c7c16231a0b6@hms.harvard.edu> <3502496E-6BAC-4571-B012-A00F8BE16D74@virginia.edu> Message-ID: When I moved to Tiger on my powerbook, I just did a straightforward update, then applied the Java 1.5 update manually (since SU never saw it). The path to Java is still /System/Library/Frameworks/JavaVM.framework/Versions then there are the following version directories: lrwxr-xr-x 1 root wheel 5 Apr 30 14:51 1.3 -> 1.3.1 drwxr-xr-x 8 root wheel 272 Apr 30 14:51 1.3.1 lrwxr-xr-x 1 root wheel 5 Apr 30 14:51 1.4 -> 1.4.2 drwxr-xr-x 8 root wheel 272 Jan 26 15:22 1.4.2 lrwxr-xr-x 1 root wheel 5 May 12 11:15 1.5 -> 1.5.0 drwxr-xr-x 8 root wheel 272 May 12 11:15 1.5.0 drwxr-xr-x 6 root wheel 204 May 16 19:47 A lrwxr-xr-x 1 root wheel 1 Apr 30 14:51 Current -> A lrwxr-xr-x 1 root wheel 5 Apr 30 14:51 CurrentJDK - > 1.4.2 When I recompiled jemboss/EMBOSS (standalone installation) with the new developers tools, I used /System/Library/Frameworks/JavaVM.framework/Versions/1.4.2 I tried compiling with 1.5, but got all sorts of java errors when I tried to launch jemboss. Michael ____________________________________________ Michael B. Black, Ph.D. Molecular Biology Computing Support ITC-ACHS, MSB rm.3013 982-4039 mblack at virginia.edu Web support, see the Molecular Biology section at: http://www.itc.virginia.edu/achs ____________________________________________ On May 26, 2005, at 6:32 AM, Koen van der Drift wrote: > > On May 25, 2005, at 7:47 PM, Michael Black wrote: > > >> When you update to Tiger, be sure to check the install option for >> the new X11, and then, install the developers tools and the new >> X11 SDK. And with Tiger, do NOT point the jemboss install script >> to Java 1.5, stick with 1.4.2, or even 1.3. >> >> > > Michael, > > What is the complete path to 1.4.2 on Tiger (on 10.3 it is "/System/ > Library/Frameworks/JavaVM.framework/Versions/1.4.2") ? I am the > maintainer of the emboss package for fink and want to make sure > that 1.5 is not used. > > > thanks, > > - Koen. > > From Richard.Rothery at ualberta.ca Thu May 26 11:33:53 2005 From: Richard.Rothery at ualberta.ca (Richard Rothery) Date: Thu, 26 May 2005 09:33:53 -0600 Subject: [EMBOSS] EMBOSS database configurartion...... Message-ID: <000001c56208$52d9e800$5e068081@Nordegg> Hi All, How does one configuire EMBOSS to retrieve sequences directly from swissprot/trembl? Specifically what lines have to be added to the database configuration file? Something that links to the EXPASY site? The idea here is to use SEQRET to grab the sequences. I have no room on my system for the entire database, indexing etc... Hopefully, the answer to this one will be simple!! Thanks, Richard ############################################### CIHR Membrane Protein Research Group, Department of Biochemistry, University of Alberta, Edmonton T6G 2H7 Ph. (780) 492-2229 Fax. (780) 492-0886 ############################################### -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20050526/aad5f4f8/attachment.html From pmr at ebi.ac.uk Thu May 26 12:39:25 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 26 May 2005 17:39:25 +0100 Subject: [EMBOSS] EMBOSS database configurartion...... In-Reply-To: <000001c56208$52d9e800$5e068081@Nordegg> References: <000001c56208$52d9e800$5e068081@Nordegg> Message-ID: <4295FBBD.7040302@ebi.ac.uk> Richard Rothery wrote: > How does one configuire EMBOSS to retrieve sequences directly from > swissprot/trembl? Specifically what lines have to be added to the > database configuration file? Something that links to the EXPASY site? > The idea here is to use SEQRET to grab the sequences. I have no room on > my system for the entire database, indexing etc... Using the EBI SRS server ... depends on which database you would like: DB uniprot [ type: P format: swiss method: srswww dbalias: uniprot url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz" ] DB sptrembl [ type: P format: swiss method: srswww dbalias: sptrembl url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz" ] DB swissprot [ type: P format: swiss method: srswww dbalias: swissprot url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz" ] Using EXPASY's SRS server (in the USA): Note the spelling of the database alias with an underscore DB expasy [ type: P format: swiss method: srswww dbalias: swiss_prot url: "http://us.expasy.org/srs5bin/cgi-bin/wgetz" ] These will all search by ID and accession number > Hopefully, the answer to this one will be simple!! There will be many possible answers. These were just a few suggestions! regards, Peter Rice From stefanielager at fastmail.ca Fri May 27 02:06:50 2005 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Fri, 27 May 2005 06:06:50 +0000 (UTC) Subject: [EMBOSS] EMBOSS database configurartion...... In-Reply-To: <4295FBBD.7040302@ebi.ac.uk> Message-ID: <20050527060650.AB45A86163E@mail.interchange.ca> Using method: URL you can also retrive entries from Swissprot (or UniProt) from http://www.ebi.uniprot.org or via dbfetch http://www.ebi.ac.uk/cgi-bin/dbfetch Stefanie > Richard Rothery wrote: > >> How does one configuire EMBOSS to retrieve sequences directly from >> swissprot/trembl? Specifically what lines have to be added to the >> database configuration file? Something that links to the EXPASY site? >> The idea here is to use SEQRET to grab the sequences. I have no room >> on my system for the entire database, indexing etc... > > Using the EBI SRS server ... depends on which database you would like: > > DB uniprot [ > type: P > format: swiss > method: srswww > dbalias: uniprot > url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz" > ] > > DB sptrembl [ > type: P > format: swiss > method: srswww > dbalias: sptrembl > url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz" > ] > > DB swissprot [ > type: P > format: swiss > method: srswww > dbalias: swissprot > url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz" > ] > > Using EXPASY's SRS server (in the USA): > > Note the spelling of the database alias with an underscore > > DB expasy [ > type: P > format: swiss > method: srswww > dbalias: swiss_prot > url: "http://us.expasy.org/srs5bin/cgi-bin/wgetz" > ] > > These will all search by ID and accession number > > >> Hopefully, the answer to this one will be simple!! > > There will be many possible answers. These were just a few > suggestions! > > > regards, > > Peter Rice _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From jmuehlis at uni-muenster.de Mon May 9 14:33:25 2005 From: jmuehlis at uni-muenster.de (Joerg Muehlisch) Date: Mon, 9 May 2005 16:33:25 +0200 Subject: [EMBOSS] emboss installation Message-ID: <200505091633.25818.jmuehlis@uni-muenster.de> Hi over there. I am just trying to install Emboss again, now under SUSE 9.2. After installing the package xdevel, that I found out to be needed, configure stops here and I can not find out how to solve this: EMBOSS-2.10.0> ./configure checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for gawk... (cached) gawk checking for gcc... cpp checking for C compiler default output file name... b.out checking whether the C compiler works... configure: error: cannot runC compiled programs. If you meant to cross compile, use `--host'. See `config.log' for more details. May be somebody ran into the same problem or knows how to solve this anyway. I did not have this problem the last time or easily found the solution... So thanks for your help, Jorg Muhlisch a user From simon.andrews at bbsrc.ac.uk Tue May 10 07:29:01 2005 From: simon.andrews at bbsrc.ac.uk (simon andrews (BI)) Date: Tue, 10 May 2005 08:29:01 +0100 Subject: [EMBOSS] emboss installation In-Reply-To: <200505091633.25818.jmuehlis@uni-muenster.de> References: <200505091633.25818.jmuehlis@uni-muenster.de> Message-ID: <1caeeea0856ae5ea9428290325f16922@bbsrc.ac.uk> On 9 May 2005, at 15:33, Joerg Muehlisch wrote: > Hi over there. > > I am just trying to install Emboss again, now under SUSE 9.2. After > installing > the package xdevel, that I found out to be needed, configure stops > here and I > can not find out how to solve this: > > EMBOSS-2.10.0> ./configure > checking for a BSD-compatible install... /usr/bin/install -c > checking whether build environment is sane... yes > checking for gawk... gawk > checking whether make sets $(MAKE)... yes > checking for gawk... (cached) gawk > checking for gcc... cpp This looks wrong. Configure is looking for gcc (a c compiler) but is getting cpp (the C preprocessor). You should install gcc and try to run configure again. If gcc is already installed then check that your CC environment variable hasn't been set to something odd as this will override the autodetection of the c compiler in configure. Simon. -- Simon Andrews PhD Bioinformatics Dept. The Babraham Institute simon.andrews at bbsrc.ac.uk +44 (0) 1223 496463 From cquijano at iib.uam.es Tue May 10 08:54:04 2005 From: cquijano at iib.uam.es (Carlos Quijano) Date: Tue, 10 May 2005 10:54:04 +0200 Subject: [EMBOSS] emboss installation In-Reply-To: <1caeeea0856ae5ea9428290325f16922@bbsrc.ac.uk> References: <200505091633.25818.jmuehlis@uni-muenster.de> <1caeeea0856ae5ea9428290325f16922@bbsrc.ac.uk> Message-ID: <1115715244.9058.37.camel@furthermore.iib.uam.es> Perhaps I will go a little bit out of the thread, but as excange I give some ideas related with it first, and then I say what I actually want to share/advice. With the simple output of ./configure is not possible to know how exactly happens your crash, and I will give no more info than Simon. But I suspect that the problem is in your development libraries (you miss something). Do what the crash-output tells you and study the installation "log", if necessary, use special verbose options in ./configure to investigate further. Luck! As far as I know, there are not current binaries for v2.10, so perhaps it is the reason for you to compile the sources. I suposse anyway that Gentoo will provide v2.10 Emboss sources soon and then you would only need to use Gentoo. (http://packages.gentoo.org/search/?sstring=emboss) You can even try to install emboss 2.10 gentoo sources right now, having in mind that you would have to unmask it from portage because it is in testing phase by this very moment. I love to compile and patch from sources... Gentoo is great for this! Debian too. If you are to habitually compile lots of packages by yourself I recommend you Gentoo. If not, Debian, that you can install from binaries easier and afterwards some packages from source when you need it. Currently, I am a happy man with Gentoo. My workstation is now my friend, not my nightmare. And I dont need to get crazy before planning a whole system upgrade, and neither after... I only wanted to share my happiness, sorry for the somewhat offtopic mail... :D Carlos. El mar, 10-05-2005 a las 08:29 +0100, simon andrews escribi?: > On 9 May 2005, at 15:33, Joerg Muehlisch wrote: > > > Hi over there. > > > > I am just trying to install Emboss again, now under SUSE 9.2. After > > installing > > the package xdevel, that I found out to be needed, configure stops > > here and I > > can not find out how to solve this: > > > > EMBOSS-2.10.0> ./configure > > checking for a BSD-compatible install... /usr/bin/install -c > > checking whether build environment is sane... yes > > checking for gawk... gawk > > checking whether make sets $(MAKE)... yes > > checking for gawk... (cached) gawk > > checking for gcc... cpp > > This looks wrong. Configure is looking for gcc (a c compiler) but is > getting cpp (the C preprocessor). You should install gcc and try to > run configure again. > > If gcc is already installed then check that your CC environment > variable hasn't been set to something odd as this will override the > autodetection of the c compiler in configure. > > Simon. From jmuehlis at uni-muenster.de Tue May 10 09:40:46 2005 From: jmuehlis at uni-muenster.de (Joerg Muehlisch) Date: Tue, 10 May 2005 11:40:46 +0200 Subject: [EMBOSS] Installation Message-ID: <200505101140.46471.jmuehlis@uni-muenster.de> Hello, I knew it would be a very simple silly mistake..., but I could not find it. Know having the compiler installed in fact it works working fine. I just remember the last time I installed there was a SUSE specific compiler that was not called gcc and was not found by configure, so I remember I had to introduce it as recommended in the script and this time I chose CC= cpp, what is obviously wrong. So I am very sorry to bother you with a simple problem like that. May be it would be a good idea to add these hints for the "users" wanting to install emboss on SUSE 9.2: 1. Install xdev package xdevel (not to find with xdev in Yast) 2. Install gcc (in former versions of SUSE this was standard) 3. Set a path variable for the libs in /usr/locale/lib?, because: >wossname wossname: error while loading shared libraries: libnucleus.so.0: cannot open shared object file: No such file or directory What would be the correct place to define that? I know this is more linux than emboss question, but as a simple user... I hope that anybody can help me with this last point, so that I will be able to work with start working with emboss again. I d like to thank everybody who is helping with this software, as it is very useful to me. I thank everybody for the help and apologize for the inconveniences. Jorg Muhlisch off topic: I m just used to work with SUSE... so it is the easiest way to me. From jmuehlis at uni-muenster.de Tue May 10 10:06:41 2005 From: jmuehlis at uni-muenster.de (Joerg Muehlisch) Date: Tue, 10 May 2005 12:06:41 +0200 Subject: [EMBOSS] emboss installation Message-ID: <200505101206.41413.jmuehlis@uni-muenster.de> Hello, I was to fast again in submitting my problem. After a restart everything works fine. Maybe the variables were not acualized for this console window... Thanks anyway for the help Jorg Muhlisch From andrespinzon at gmail.com Tue May 10 17:26:34 2005 From: andrespinzon at gmail.com (Andres Pinzon) Date: Tue, 10 May 2005 12:26:34 -0500 Subject: [EMBOSS] Installation In-Reply-To: <200505101140.46471.jmuehlis@uni-muenster.de> References: <200505101140.46471.jmuehlis@uni-muenster.de> Message-ID: <8968fc7e05051010265b436a4@mail.gmail.com> 2005/5/10, Joerg Muehlisch : > Hello, > wossname: error while loading shared libraries: libnucleus.so.0: cannot open > shared object file: No such file or directory > What would be the correct place to define that? > I know this is more linux than emboss question, but as a simple user... if im not wrong, libnucleus is part of the EMBOSS installation, and it should be in /usr/local/emboss/lib if u installed emboss in that path. > off topic: > I m just used to work with SUSE... so it is the easiest way to me. Hey, dont worry about that, i have 2 emboss installations in SUSE9.2 and it works just fine!!!! At home I use Slackware, but at my Job Im in charge of 4 machines and 3 of them run SUSE, it rocks anyway. -- --------- Andr?s Pinz?n [http://www.andrespinzon.com] Centro de Bioinformatica, Instituto de Biotecnologia http://bioinf.ibun.unal.edu.co Universidad Nacional de Colombia tel. 3165000 ext. 16961 GNU/Linux user number 349752 ---------- From gbottu at ben.vub.ac.be Wed May 18 16:35:56 2005 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Wed, 18 May 2005 18:35:56 +0200 Subject: [EMBOSS] question about PRINTS Message-ID: <20050518163556.GA28052@bigben.ulb.ac.be> Dear colleagues, I have a question about the PRINTS database (needed for the program pscan). I have noticed that there have been no updates since already almost 2 years. Did they give up the maintenance ? Does someone know more about this ? Guy Bottu, BEN From rls at ebi.ac.uk Wed May 18 18:48:00 2005 From: rls at ebi.ac.uk (Rodrigo Lopez) Date: Wed, 18 May 2005 19:48:00 +0100 Subject: [EMBOSS] question about PRINTS In-Reply-To: <20050518163556.GA28052@bigben.ulb.ac.be> Message-ID: <001601c55bda$1ebb80d0$0fd81452@castafiore> You should contact Terry Attwood (attwood at bioinf.man.ac.uk) about PRINTS. R:) > -----Original Message----- > From: owner-emboss at hgmp.mrc.ac.uk > [mailto:owner-emboss at hgmp.mrc.ac.uk] On Behalf Of Guy Bottu > Sent: 18 May 2005 17:36 > To: emboss at embnet.org > Subject: [EMBOSS] question about PRINTS > > > Dear colleagues, > > I have a question about the PRINTS database (needed for the program > pscan). I have noticed that there have been no updates since already > almost 2 years. Did they give up the maintenance ? Does > someone know more > about this ? > > Guy Bottu, > BEN > From isabelle.wells at roche.com Thu May 19 15:12:00 2005 From: isabelle.wells at roche.com (Wells, Isabelle) Date: Thu, 19 May 2005 17:12:00 +0200 Subject: [EMBOSS] Help with retrieving the indexing date Message-ID: <062896243F02D445AB77BD2B51E2F3738898B1@rbamsem3.emea.roche.com> Hello all, I am using dbiflat to index our databases with the option -date dd/mm/yy. It seems this date should be stored in the binary index files. Is there a way or a tool to extract this date from the file? Thanks for your help, > Isabelle > +--- O---O ------------------------------------------- o-o Isabelle Wells, Ph. D. O F. Hoffmann-La Roche Ltd o-o Bioinformatics o---o PRBI-P, building 65/307 o----o CH-4070 Basel, Switzerland O----O 0--o O o-o E-mail: isabelle.wells at roche.com +- o---o --------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From pmr at ebi.ac.uk Thu May 19 15:37:06 2005 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Thu, 19 May 2005 16:37:06 +0100 (BST) Subject: [EMBOSS] Help with retrieving the indexing date In-Reply-To: <062896243F02D445AB77BD2B51E2F3738898B1@rbamsem3.emea.roche.com> References: <062896243F02D445AB77BD2B51E2F3738898B1@rbamsem3.emea.roche.com> Message-ID: <1647.128.211.168.136.1116517026.squirrel@webmail.ebi.ac.uk> Hi Isabelle, > I am using dbiflat to index our databases with the option -date > dd/mm/yy. It seems this date should be stored in the binary index files. > Is there a way or a tool to extract this date from the file? > Thanks for your help, There is a script that is included in the scripts directory for debugging. I would like to extract information such as the index data when retrieving sequences and in showdb, but it is complicated because only the EMBLCD databases (index by dbiflat and the other dbi tools in EMBOSS) have the date easily available. We could, perhaps, try to get the date for SRS and SRSWWW and SRSFASTA databases. We could also look into retrieving dates from the new indexing system under development to replace EMBLCD (and dbiflat). How useful would this be? Perhaps as an extra option to showdb, because it will be slow to retrieve the information from a lareg number of external databases. Hope this helps, Peter Rice From isabelle.wells at roche.com Fri May 20 08:39:21 2005 From: isabelle.wells at roche.com (Wells, Isabelle) Date: Fri, 20 May 2005 10:39:21 +0200 Subject: [EMBOSS] Help with retrieving the indexing date Message-ID: <062896243F02D445AB77BD2B51E2F3738AE8EF@rbamsem3.emea.roche.com> Hi Peter, Thanks very much for the info. We found the script and were able to write a program which reads this date. We don't have SRS databases but an extra option in showdb to show the date would have been useful. Best regards, Isabelle -----Original Message----- From: pmr at ebi.ac.uk [mailto:pmr at ebi.ac.uk] Sent: Thursday, May 19, 2005 17:37 To: Wells, Isabelle {PRBI~Basel} Cc: emboss at embnet.org Subject: Re: [EMBOSS] Help with retrieving the indexing date Hi Isabelle, > I am using dbiflat to index our databases with the option -date > dd/mm/yy. It seems this date should be stored in the binary index > files. Is there a way or a tool to extract this date from the file? > Thanks for your help, There is a script that is included in the scripts directory for debugging. I would like to extract information such as the index data when retrieving sequences and in showdb, but it is complicated because only the EMBLCD databases (index by dbiflat and the other dbi tools in EMBOSS) have the date easily available. We could, perhaps, try to get the date for SRS and SRSWWW and SRSFASTA databases. We could also look into retrieving dates from the new indexing system under development to replace EMBLCD (and dbiflat). How useful would this be? Perhaps as an extra option to showdb, because it will be slow to retrieve the information from a lareg number of external databases. Hope this helps, Peter Rice From atorrano at lsi.upc.edu Fri May 20 10:52:33 2005 From: atorrano at lsi.upc.edu (Alexis Torrano Martinez) Date: Fri, 20 May 2005 12:52:33 +0200 (MET DST) Subject: [EMBOSS] seqret Message-ID: <7462737191atorrano@lsi.upc.es> Hello. I have just begun to use emboss. I'd like to ask some question. Let the next tuple be my DB descriptor : DB myDB [ dir: /..../myDBdir indexdirectory: /..../indexesForMyDB ] Is it possible to split the DB through different directories or disks? On two 300Gb disks mounted on /mnt/d1 and /mnt/d2, I put some files on d1 and the other on d2... so, a tuple like the next, would it be correct? DB myDB [ dir: /mnt/d1/myDB dir: /mnt/d2/myDB indexdirectory: /..../indexesForMyDB ] or DB myDB [ dir: /mnt/d1/myDB : /mnt/d2/myDB indexdirectory: /..../indexesForMyDB ] How would be done such split?? A lot of thanks, and best regards. Alexis. From jison at hgmp.mrc.ac.uk Fri May 20 11:15:33 2005 From: jison at hgmp.mrc.ac.uk (Dr J.C. Ison) Date: Fri, 20 May 2005 12:15:33 +0100 Subject: [EMBOSS] seqret References: <7462737191atorrano@lsi.upc.es> Message-ID: <428DC6D5.97F40476@hgmp.mrc.ac.uk> Dear Alexis So far as I am aware it is not possible to split a database in that way. You would need two separate definitions for the different parts (d1/myDB and d2/myDB). Cheers Jon Alexis Torrano Martinez wrote: > > Hello. > > I have just begun to use emboss. I'd like to ask some question. > Let the next tuple be my DB descriptor : > > DB myDB [ > > dir: /..../myDBdir > indexdirectory: /..../indexesForMyDB > ] > > Is it possible to split the DB through different directories or disks? > On two 300Gb disks mounted on /mnt/d1 and /mnt/d2, I put some files on > d1 and the other on d2... so, a tuple like the next, would it be correct? > > DB myDB [ > > dir: /mnt/d1/myDB > dir: /mnt/d2/myDB > indexdirectory: /..../indexesForMyDB > ] > > or > > DB myDB [ > > dir: /mnt/d1/myDB : /mnt/d2/myDB > indexdirectory: /..../indexesForMyDB > ] > > How would be done such split?? > > A lot of thanks, and best regards. > > Alexis. -- Jon C. Ison, PhD Proteomics Applications Group MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK Tel: +44 1223 494500 Fax: +44 1223 494512 E-mail: jison at rfcgr.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk From pmr at ebi.ac.uk Fri May 20 11:39:10 2005 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Fri, 20 May 2005 12:39:10 +0100 (BST) Subject: [EMBOSS] seqret In-Reply-To: <7462737191atorrano@lsi.upc.es> References: <7462737191atorrano@lsi.upc.es> Message-ID: <1288.128.210.190.180.1116589150.squirrel@webmail.ebi.ac.uk> Dear Alexis, > Is it possible to split the DB through different directories or disks? > On two 300Gb disks mounted on /mnt/d1 and /mnt/d2, I put some files on > d1 and the other on d2... so, a tuple like the next, would it be correct? > > How would be done such split?? The indexing format we use in EMBOSS was developed for the Staden package some years ago, and has no space to store more than one directory. 1. use symbolic links - either add links to /mnt/d1 that point to the files in /mnt/d2, or create a new directory /mnt/d0 with symlinks to all the files in /mnt/d1 and /mnt/d2 2. we are working on a new indexing system where we may be able to allow multiple directories, but it does add extra complexity. We will look into the possibility. Hope that helps, regards, Peter Rice From leongmz at gmail.com Sat May 21 07:41:19 2005 From: leongmz at gmail.com (Michael Leong) Date: Sat, 21 May 2005 00:41:19 -0700 Subject: [EMBOSS] Jemboss launch killing cpu Message-ID: <6.1.2.0.2.20050521003703.02f8d6d8@ifurita.dyndns.org> Hi. I'm trying to setup Jemboss on my lan and trying to use the java webstart to launch it. However, on the Jemboss login window, when the progress meter reaches about 50%, it locks up and eats all teh cpu. Thx, mike Here are the steps at I took to install it: #------------------------------------------------------ untar EMBOSSS 2.10.0 untar tomcat 5.5.9 download emboss install script for tomcat 5.5.x untar axis 1.2 mkdir /opt/emboss-data/soap chmod 777 /opt/emboss-data/soap chmod a+t /opt/emboss-data/soap replace install script w/ one for tomcat 5.5.x run ./install-jemboss-server.sh install options: client-server os: linux ip: 192.168.2.108 ssl: yes port: 8443 java: jdk v1.5 unix auth: yes tomcat uid: 1000 auth method: shadow embassy pkgs: no clustalw: /usr/bin primer3_core: auto deploy: yes modifed server.xml as told got warning about javax.activation.DataHandler and javax.mail.internet.MimeMultipart not found chown root /opt/emboss/bin/jembossctl chmod u+s /opt/emboss/bin/jembossctl cd /opt/emboss/share/EMBOSS/jemboss/utils ./makeJNLP.sh edit /opt/emboss/share/EMBOSS/jemboss/jnlp/index.html and Jemboss.jnlp to proper webserver copy /opt/emboss/share/EMBOSS/jemboss/jnlp/* to webserver #------------------------------------------------------ From ableasby at hgmp.mrc.ac.uk Sat May 21 08:26:00 2005 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Sat, 21 May 2005 09:26:00 +0100 (BST) Subject: [EMBOSS] Jemboss launch killing cpu Message-ID: <200505210826.j4L8Q0UB014121@bromine.hgmp.mrc.ac.uk> Dear Mike, The first thing to check with those symptoms is that you are running JDK 5.0 Update 3. Previous versions of java 1.5 under linux had a JWS bug which caused such a CPU-eating problem. HTH Alan Bleasby HGMP/RFCGR (for a little while) From leongmz at gmail.com Sat May 21 09:01:21 2005 From: leongmz at gmail.com (Michael Leong) Date: Sat, 21 May 2005 02:01:21 -0700 Subject: [EMBOSS] Jemboss launch killing cpu In-Reply-To: <200505210826.j4L8Q0UB014121@bromine.hgmp.mrc.ac.uk> References: <200505210826.j4L8Q0UB014121@bromine.hgmp.mrc.ac.uk> Message-ID: <6.1.2.0.2.20050521015918.02f790c8@pop.gmail.com> Still same problem after I upgarded. server: linux 2.4.27-om-20040808, jdk 1.50, update3 client : windows 2000, jre 1.50, updatae 3 At 01:26 AM 5/21/2005, Alan Bleasby wrote: >Dear Mike, > >The first thing to check with those symptoms is that you >are running JDK 5.0 Update 3. Previous versions of java 1.5 >under linux had a JWS bug which caused such a CPU-eating >problem. > >HTH > >Alan Bleasby >HGMP/RFCGR (for a little while) From leongmz at gmail.com Sat May 21 10:05:36 2005 From: leongmz at gmail.com (Michael Leong) Date: Sat, 21 May 2005 03:05:36 -0700 Subject: [EMBOSS] Jemboss launch killing cpu In-Reply-To: <200505210923.j4L9NGO7006557@bromine.hgmp.mrc.ac.uk> References: <200505210923.j4L9NGO7006557@bromine.hgmp.mrc.ac.uk> Message-ID: <6.1.2.0.2.20050521030142.02ebe478@pop.gmail.com> Grr.. this is bad. Every jre/os combination drained the cpu. w2k/jre 1.5, update 2 w2k/jre 1.5, update 3 w2k/jre 1.4.2 update 8 linux/jre 1.5, update 3 Are there another gui cflient equalivent to jemboss (functionality, support, etc) thx, mike At 02:23 AM 5/21/2005, Alan Bleasby wrote: >Dear Mike, > >The JWS bug would have affected a linux client but yours looks >to be a windows one. I assume the CPU-eating is happening on >the client? > >I'm CCing this to Tim Carver (jemboss author) who, I believe, >gets back from holiday this weekend. He may be able to help. > >Alan Bleasby > > >Hi. > >I'm trying to setup Jemboss on my lan and trying to use the java webstart >to launch it. However, on the Jemboss login window, when the progress >meter reaches about 50%, it locks up and eats all teh cpu. > >Thx, >mike > >Here are the steps at I took to install it: > >#------------------------------------------------------ >untar EMBOSSS 2.10.0 >untar tomcat 5.5.9 >download emboss install script for tomcat 5.5.x >untar axis 1.2 >mkdir /opt/emboss-data/soap >chmod 777 /opt/emboss-data/soap >chmod a+t /opt/emboss-data/soap > >replace install script w/ one for tomcat 5.5.x >run ./install-jemboss-server.sh > >install options: >client-server >os: linux >ip: 192.168.2.108 >ssl: yes >port: 8443 >java: jdk v1.5 >unix auth: yes >tomcat uid: 1000 >auth method: shadow >embassy pkgs: no >clustalw: /usr/bin >primer3_core: >auto deploy: yes >modifed server.xml as told >got warning about javax.activation.DataHandler and >javax.mail.internet.MimeMultipart not found > > chown root /opt/emboss/bin/jembossctl > chmod u+s /opt/emboss/bin/jembossctl > >cd /opt/emboss/share/EMBOSS/jemboss/utils >./makeJNLP.sh > >edit /opt/emboss/share/EMBOSS/jemboss/jnlp/index.html and Jemboss.jnlp to >proper webserver > >copy /opt/emboss/share/EMBOSS/jemboss/jnlp/* to webserver >#------------------------------------------------------ From ableasby at hgmp.mrc.ac.uk Sat May 21 10:49:14 2005 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Sat, 21 May 2005 11:49:14 +0100 (BST) Subject: [EMBOSS] Jemboss launch killing cpu Message-ID: <200505211049.j4LAnE8m010022@bromine.hgmp.mrc.ac.uk> >Are there another gui cflient equalivent to jemboss No, all interfaces have their different strengths and weaknesses. For other interfaces see: http://emboss.sourceforge.net/interfaces/#interfaces We will be doing an in depth GUI survey in the near future. [oh, and I'd appreciate it if email I sent to you off-list was not posted back to the list. Thanks] HTH Alan Bleasby HGMP/RFCGR From leongmz at gmail.com Sat May 21 19:26:56 2005 From: leongmz at gmail.com (Michael Leong) Date: Sat, 21 May 2005 12:26:56 -0700 Subject: [EMBOSS] Jemboss launch killing cpu In-Reply-To: <200505211049.j4LAnE8m010022@bromine.hgmp.mrc.ac.uk> References: <200505211049.j4LAnE8m010022@bromine.hgmp.mrc.ac.uk> Message-ID: <6.1.2.0.2.20050521122601.02eca198@pop.gmail.com> At 03:49 AM 5/21/2005, Alan Bleasby wrote: > >Are there another gui cflient equalivent to jemboss > >No, all interfaces have their different strengths and weaknesses. >For other interfaces see: > http://emboss.sourceforge.net/interfaces/#interfaces > >We will be doing an in depth GUI survey in the near future. > >[oh, and I'd appreciate it if email I sent to you off-list was not > posted back to the list. Thanks] my apologies. mike >HTH > >Alan Bleasby >HGMP/RFCGR From leongmz at gmail.com Sun May 22 20:02:04 2005 From: leongmz at gmail.com (Michael Leong) Date: Sun, 22 May 2005 13:02:04 -0700 Subject: [EMBOSS] Jemboss Login problem Message-ID: <6.1.2.0.2.20050522125831.02f4ef40@ifurita.dyndns.org> Hi, I got Jemboss running on my lan, but it keep saying my login is incorrect. I've used the install-jemboss-server.sh script to install the entire pkg. auth method is linux/shadow. The tomcat user has permission to read /etc/shadow. setting: java: 1.4.2_8 tomcat: 5.0.30 axis: 1.1 emboss: 2.9.0 w/ the Jemboss patches. os: linux auth: shadow thx, mike From leongmz at gmail.com Sun May 22 22:30:10 2005 From: leongmz at gmail.com (Michael Leong) Date: Sun, 22 May 2005 15:30:10 -0700 Subject: [EMBOSS] Jemboss Login problem In-Reply-To: <6.1.2.0.2.20050522125831.02f4ef40@ifurita.dyndns.org> References: <6.1.2.0.2.20050522125831.02f4ef40@ifurita.dyndns.org> Message-ID: <6.1.2.0.2.20050522145328.02f226b8@pop.gmail.com> Got the following error on jemboss_error.log w/ shadow: Failed Authorisation mike STDERR java_pipe_read timeout java_rcv error Pipe Recv error 1 with pam: Failed Authorisation mike STDERR Other than that, can't find any thing else on At 01:02 PM 5/22/2005, Michael Leong wrote: >Hi, > >I got Jemboss running on my lan, but it keep saying my login is incorrect. > >I've used the install-jemboss-server.sh script to install the entire pkg. > >auth method is linux/shadow. The tomcat user has permission to read >/etc/shadow. > > >setting: >java: 1.4.2_8 >tomcat: 5.0.30 >axis: 1.1 >emboss: 2.9.0 w/ the Jemboss patches. >os: linux >auth: shadow > > >thx, > >mike > From asonyadi at cp.co.id Mon May 23 00:55:43 2005 From: asonyadi at cp.co.id (Sony Adi Susanto) Date: Mon, 23 May 2005 07:55:43 +0700 Subject: [EMBOSS] please unsubscribe Message-ID: Biotechnology Department Research & Development Center, PT Charoen Pokphand Indonesia Tbk Jl. Parangtritis Raya Blok A-5E No.12A Ancol Barat, Jakarta, DKI Jakarta Indonesia Telp : 62-251-6926241 Fax : 62-351-6930364 Email address : asonyadi at cp.co.id; asonyadi at yahoo.com.sg -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeremy at biochem.uthscsa.edu Wed May 25 15:59:19 2005 From: jeremy at biochem.uthscsa.edu (Jeremy Mann) Date: Wed, 25 May 2005 10:59:19 -0500 (CDT) Subject: [EMBOSS] Installation help Message-ID: <46609.129.111.174.49.1117036759.squirrel@biochem.uthscsa.edu> I am having a very difficult time getting the EMBOSS client/server install on a Suse Linux 9.1 system. I have followed the instructions precisely. Tomcat starts, then gives me this error. Note I have also tried this with the newer 5.5.9 Tomcat (with new install file) and this still happens: Please wait, starting tomcat....... Using CATALINA_BASE: /usr/local/jakarta-tomcat-5.0.30 Using CATALINA_HOME: /usr/local/jakarta-tomcat-5.0.30 Using CATALINA_TMPDIR: /usr/local/jakarta-tomcat-5.0.30/temp Using JAVA_HOME: /usr/lib/java May 25, 2005 10:27:53 AM org.apache.axis.utils.JavaUtils isAttachmentSupported WARNING: Unable to find required classes (javax.activation.DataHandler and javax.mail.internet.MimeMultipart). Attachment support is disabled. Processing file JembossServer.wsdd Exception: AxisFault faultCode: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException faultSubcode: faultString: java.net.ConnectException: Connection refused faultActor: faultNode: faultDetail: {http://xml.apache.org/axis/}stackTrace:java.net.ConnectException: Connection refused at java.net.PlainSocketImpl.socketConnect(Native Method) at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:305) at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:171) at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:158) at java.net.Socket.connect(Socket.java:452) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:324) at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFactory.java:135) at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFactory.java:99) at org.apache.axis.transport.http.HTTPSender.getSocket(HTTPSender.java:130) at org.apache.axis.transport.http.HTTPSender.writeToSocket(HTTPSender.java:382) at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:88) at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32) at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118) at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83) at org.apache.axis.client.AxisClient.invoke(AxisClient.java:147) at org.apache.axis.client.Call.invokeEngine(Call.java:2737) at org.apache.axis.client.Call.invoke(Call.java:2720) at org.apache.axis.client.Call.invoke(Call.java:1756) at org.apache.axis.client.AdminClient.process(AdminClient.java:438) at org.apache.axis.client.AdminClient.process(AdminClient.java:403) at org.apache.axis.client.AdminClient.process(AdminClient.java:409) at org.apache.axis.client.AdminClient.process(AdminClient.java:319) at org.apache.axis.client.AdminClient.main(AdminClient.java:462) {http://xml.apache.org/axis/}hostname:bcf Tomcat is active on port 8080, even though I told the install script to use 8443. Also, there is no Axis service for emboss, only version and admin. What is going wrong with my installation? -- 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 robin at hms.harvard.edu Wed May 25 17:33:50 2005 From: robin at hms.harvard.edu (Robin Colgrove) Date: Wed, 25 May 2005 13:33:50 -0400 Subject: [EMBOSS] Installation help In-Reply-To: <46609.129.111.174.49.1117036759.squirrel@biochem.uthscsa.edu> References: <46609.129.111.174.49.1117036759.squirrel@biochem.uthscsa.edu> Message-ID: <70a549240c9938139675c7c16231a0b6@hms.harvard.edu> Hello all, After numerous attempts following suggestions on this list, I never have been able to get the X11 version of EMBOSS to install on my iBook under Mac OS X 10.3.8, but I installed and have been using the command line version without trouble (and using the GUI programs remotely with EMBOSS on a server and running the Mac X11 client locally). Next week I am going to upgrade to OSX 10.4 "Tiger", and was thinking of trying a full EMBOSS install again. I would be interested to hear from anyone who has done this (EMBOSS on Tiger) and any tips/advice. Also, it is not clear to me whether it would be best to uninstall everything and reinstall, or whether I could just install the X11 parts over an existing install. thanks Robin Colgrove Dept of Microbiology Harvard Medical School From leongmz at gmail.com Wed May 25 18:06:47 2005 From: leongmz at gmail.com (Michael Leong) Date: Wed, 25 May 2005 11:06:47 -0700 Subject: [EMBOSS] Installation help In-Reply-To: <46609.129.111.174.49.1117036759.squirrel@biochem.uthscsa.e du> References: <46609.129.111.174.49.1117036759.squirrel@biochem.uthscsa.edu> Message-ID: <6.1.2.0.2.20050525110553.02dd03d0@pop.gmail.com> If you're using tomcat 5.5.9, get the newer install-jemboss-server.sh script from the website. mike At 08:59 AM 5/25/2005, Jeremy Mann wrote: >I am having a very difficult time getting the EMBOSS client/server install >on a Suse Linux 9.1 system. I have followed the instructions precisely. >Tomcat starts, then gives me this error. Note I have also tried this with >the newer 5.5.9 Tomcat (with new install file) and this still happens: > >Please wait, starting tomcat....... >Using CATALINA_BASE: /usr/local/jakarta-tomcat-5.0.30 >Using CATALINA_HOME: /usr/local/jakarta-tomcat-5.0.30 >Using CATALINA_TMPDIR: /usr/local/jakarta-tomcat-5.0.30/temp >Using JAVA_HOME: /usr/lib/java > > >May 25, 2005 10:27:53 AM org.apache.axis.utils.JavaUtils >isAttachmentSupported >WARNING: Unable to find required classes (javax.activation.DataHandler and >javax.mail.internet.MimeMultipart). Attachment support is disabled. >Processing file JembossServer.wsdd >Exception: AxisFault > faultCode: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException > faultSubcode: > faultString: java.net.ConnectException: Connection refused > faultActor: > faultNode: > faultDetail: > {http://xml.apache.org/axis/}stackTrace:java.net.ConnectException: >Connection refused > at java.net.PlainSocketImpl.socketConnect(Native Method) > at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:305) > at >java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:171) > at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:158) > at java.net.Socket.connect(Socket.java:452) > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at >sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) > at >sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) > at java.lang.reflect.Method.invoke(Method.java:324) > at >org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFactory.java:135) > at >org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFactory.java:99) > at >org.apache.axis.transport.http.HTTPSender.getSocket(HTTPSender.java:130) > at >org.apache.axis.transport.http.HTTPSender.writeToSocket(HTTPSender.java:382) > at >org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:88) > at >org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32) > at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118) > at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83) > at org.apache.axis.client.AxisClient.invoke(AxisClient.java:147) > at org.apache.axis.client.Call.invokeEngine(Call.java:2737) > at org.apache.axis.client.Call.invoke(Call.java:2720) > at org.apache.axis.client.Call.invoke(Call.java:1756) > at org.apache.axis.client.AdminClient.process(AdminClient.java:438) > at org.apache.axis.client.AdminClient.process(AdminClient.java:403) > at org.apache.axis.client.AdminClient.process(AdminClient.java:409) > at org.apache.axis.client.AdminClient.process(AdminClient.java:319) > at org.apache.axis.client.AdminClient.main(AdminClient.java:462) > > {http://xml.apache.org/axis/}hostname:bcf > >Tomcat is active on port 8080, even though I told the install script to >use 8443. Also, there is no Axis service for emboss, only version and >admin. > >What is going wrong with my installation? > > > > >-- >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 jeremy at biochem.uthscsa.edu Wed May 25 18:31:12 2005 From: jeremy at biochem.uthscsa.edu (Jeremy Mann) Date: Wed, 25 May 2005 13:31:12 -0500 (CDT) Subject: [EMBOSS] Installation help In-Reply-To: References: <46609.129.111.174.49.1117036759.squirrel@biochem.uthscsa.edu> Message-ID: <50678.129.111.174.49.1117045872.squirrel@biochem.uthscsa.edu> Tim Carver said: > Hi Jeremy > > If tomcat is not using 8443 then the deployment of the Jemboss services > will fail. When you run the script you are asked to cut and paste lines > into conf/server.xml. Did you do this? Are there any error in the tomcat > logs/catalina.out. > > Btw, running the script from scratch will mean that you need a fresh copy > of tomcat, EMBOSS and axis and you will need to remove the previous EMBOSS > installation directories. I just tried again for the 6th time. Yes, I copy pasted the lines to the bottom of server.xml. Catalina.out: Created MBeanServer with ID: 147c5fc:104151818da:-8000:bcf:1 May 25, 2005 1:23:18 PM org.apache.tomcat.util.digester.Digester fatalError SEVERE: Parse Fatal Error at line 380 column 6: The markup in the document following the root element must be well-formed. org.xml.sax.SAXParseException: The markup in the document following the root element must be well-formed. at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source) at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source) at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source) at org.apache.xerces.impl.XMLDocumentScannerImpl$TrailingMiscDispatcher.dispatch(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) at org.apache.tomcat.util.digester.Digester.parse(Digester.java:1561) at org.apache.catalina.startup.Catalina.load(Catalina.java:473) at org.apache.catalina.startup.Catalina.load(Catalina.java:509) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:324) at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:243) at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:408) May 25, 2005 1:23:18 PM org.apache.catalina.startup.Catalina load WARNING: Catalina.start using conf/server.xml: org.xml.sax.SAXParseException: The markup in the document following the root element must be well-formed. at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) at org.apache.tomcat.util.digester.Digester.parse(Digester.java:1561) at org.apache.catalina.startup.Catalina.load(Catalina.java:473) at org.apache.catalina.startup.Catalina.load(Catalina.java:509) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:324) at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:243) at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:408) May 25, 2005 1:23:18 PM org.apache.coyote.http11.Http11Protocol init INFO: Initializing Coyote HTTP/1.1 on http-8080 May 25, 2005 1:23:18 PM org.apache.catalina.core.StandardService start INFO: Starting service Catalina May 25, 2005 1:23:18 PM org.apache.catalina.core.StandardEngine start INFO: Starting Servlet Engine: Apache Tomcat/5.5.9 May 25, 2005 1:23:18 PM org.apache.catalina.core.StandardHost start INFO: XML validation disabled - Unable to find config file. Creating new servlet engine config file: /WEB-INF/server-config.wsdd May 25, 2005 1:23:21 PM org.apache.coyote.http11.Http11Protocol start INFO: Starting Coyote HTTP/1.1 on http-8080 May 25, 2005 1:23:21 PM org.apache.jk.common.ChannelSocket init INFO: JK: ajp13 listening on /0.0.0.0:8009 May 25, 2005 1:23:21 PM org.apache.jk.server.JkMain start INFO: Jk running ID=0 time=0/31 config=null May 25, 2005 1:23:21 PM org.apache.catalina.storeconfig.StoreLoader load INFO: Find registry server-registry.xml at classpath resource May 25, 2005 1:23:21 PM org.apache.catalina.startup.Catalina start INFO: Server startup in 3219 ms Install script: Please wait, starting tomcat....... Using CATALINA_BASE: /usr/local/jakarta-tomcat-5.5.9 Using CATALINA_HOME: /usr/local/jakarta-tomcat-5.5.9 Using CATALINA_TMPDIR: /usr/local/jakarta-tomcat-5.5.9/temp Using JRE_HOME: /usr/lib/java/jre May 25, 2005 1:19:08 PM org.apache.axis.utils.JavaUtils isAttachmentSupported WARNING: Unable to find required classes (javax.activation.DataHandler and javax.mail.internet.MimeMultipart). Attachment support is disabled. Processing file JembossServer.wsdd Exception: AxisFault faultCode: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException faultSubcode: faultString: java.net.ConnectException: Connection refused faultActor: faultNode: faultDetail: {http://xml.apache.org/axis/}stackTrace:java.net.ConnectException: Connection refused at java.net.PlainSocketImpl.socketConnect(Native Method) at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:305) at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:171) at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:158) at java.net.Socket.connect(Socket.java:452) at com.sun.net.ssl.internal.ssl.SSLSocketImpl.connect(DashoA12275) at com.sun.net.ssl.internal.ssl.SSLSocketImpl.<init>(DashoA12275) at com.sun.net.ssl.internal.ssl.SSLSocketFactoryImpl.createSocket(DashoA12275) at org.apache.axis.components.net.JSSESocketFactory.create(JSSESocketFactory.java:92) at org.apache.axis.transport.http.HTTPSender.getSocket(HTTPSender.java:130) at org.apache.axis.transport.http.HTTPSender.writeToSocket(HTTPSender.java:382) at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:88) at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32) at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118) at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83) at org.apache.axis.client.AxisClient.invoke(AxisClient.java:147) at org.apache.axis.client.Call.invokeEngine(Call.java:2737) at org.apache.axis.client.Call.invoke(Call.java:2720) at org.apache.axis.client.Call.invoke(Call.java:1756) at org.apache.axis.client.AdminClient.process(AdminClient.java:438) at org.apache.axis.client.AdminClient.process(AdminClient.java:403) at org.apache.axis.client.AdminClient.process(AdminClient.java:409) at org.apache.axis.client.AdminClient.process(AdminClient.java:319) at org.apache.axis.client.AdminClient.main(AdminClient.java:462) {http://xml.apache.org/axis/}hostname:bcf -- 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 kvddrift at earthlink.net Wed May 25 22:20:22 2005 From: kvddrift at earthlink.net (Koen van der Drift) Date: Wed, 25 May 2005 18:20:22 -0400 Subject: [EMBOSS] Installation help In-Reply-To: <70a549240c9938139675c7c16231a0b6@hms.harvard.edu> References: <46609.129.111.174.49.1117036759.squirrel@biochem.uthscsa.edu> <70a549240c9938139675c7c16231a0b6@hms.harvard.edu> Message-ID: <870f792bbfbc294665000e811f692f44@earthlink.net> Hi Robin, Which X11 GUI are you trying to use? I have no experience yet with Tiger, but have no problems with using the kaptain GUI (installed through fink). - Koen. On May 25, 2005, at 1:33 PM, Robin Colgrove wrote: > > Hello all, > > After numerous attempts following suggestions on this list, I never > have been able to get the X11 version of EMBOSS to install on my iBook > under Mac OS X 10.3.8, but I installed and have been using the command > line version without trouble (and using the GUI programs remotely with > EMBOSS on a server and running the Mac X11 client locally). > > Next week I am going to upgrade to OSX 10.4 "Tiger", and was thinking > of trying a full EMBOSS install again. I would be interested to hear > from anyone who has done this (EMBOSS on Tiger) and any tips/advice. > Also, it is not clear to me whether it would be best to uninstall > everything and reinstall, or whether I could just install the X11 > parts over an existing install. > > thanks > > Robin Colgrove > Dept of Microbiology > Harvard Medical School > From mbb8n at virginia.edu Wed May 25 23:47:22 2005 From: mbb8n at virginia.edu (Michael Black) Date: Wed, 25 May 2005 19:47:22 -0400 Subject: [EMBOSS] Installation help In-Reply-To: <70a549240c9938139675c7c16231a0b6@hms.harvard.edu> References: <46609.129.111.174.49.1117036759.squirrel@biochem.uthscsa.edu> <70a549240c9938139675c7c16231a0b6@hms.harvard.edu> Message-ID: <3502496E-6BAC-4571-B012-A00F8BE16D74@virginia.edu> Robin, are you referring to the JemBoss installation? And do you mean a standalone installation, or a server installation? I've never had a problem installing Jemboss/EMBOSS (and the Embassy packages) standalone in Jaguar, Panther and now Tiger. PNG support requires some additional efforts (FINK takes care of that, for me). Jemboss 1.5 and EMBOSS 2.10.0 run fine on my powerbook under Tiger. I always run the jemboos installer script to install everything (embassy included), and follow the Jemboss installation guide for OS X. I also have it running fine on a dual-2.5GHz G5 running Panther 10.3.9. When you update to Tiger, be sure to check the install option for the new X11, and then, install the developers tools and the new X11 SDK. And with Tiger, do NOT point the jemboss install script to Java 1.5, stick with 1.4.2, or even 1.3. Michael ____________________________________________ Michael B. Black, Ph.D. Molecular Biology Computing Support ITC-ACHS, MSB rm.3013 982-4039 mblack at virginia.edu Web support, see the Molecular Biology section at: http://www.itc.virginia.edu/achs ____________________________________________ On May 25, 2005, at 1:33 PM, Robin Colgrove wrote: > > Hello all, > > After numerous attempts following suggestions on this list, I never > have been able to get the X11 version of EMBOSS to install on my > iBook under Mac OS X 10.3.8, but I installed and have been using > the command line version without trouble (and using the GUI > programs remotely with EMBOSS on a server and running the Mac X11 > client locally). > > Next week I am going to upgrade to OSX 10.4 "Tiger", and was > thinking of trying a full EMBOSS install again. I would be > interested to hear from anyone who has done this (EMBOSS on Tiger) > and any tips/advice. Also, it is not clear to me whether it would > be best to uninstall everything and reinstall, or whether I could > just install the X11 parts over an existing install. > > thanks > > Robin Colgrove > Dept of Microbiology > Harvard Medical School > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tjc at sanger.ac.uk Thu May 26 09:58:28 2005 From: tjc at sanger.ac.uk (Tim Carver) Date: Thu, 26 May 2005 10:58:28 +0100 (BST) Subject: [EMBOSS] Installation help (fwd) Message-ID: Thanks Michael that is useful to the EMBOSS group as we are waiting for a copy of Tiger to test Jemboss/EMBOSS out on. So it is good to know that you have it working. Also just a note that 1.3 is no longer supported, so the options are 1.4.2 or 1.5. Regards Tim Carver On Wed, 25 May 2005, Michael Black wrote: > Robin, are you referring to the JemBoss installation? And do you > mean a standalone installation, or a server installation? > > I've never had a problem installing Jemboss/EMBOSS (and the Embassy > packages) standalone in Jaguar, Panther and now Tiger. PNG support > requires some additional efforts (FINK takes care of that, for me). > Jemboss 1.5 and EMBOSS 2.10.0 run fine on my powerbook under Tiger. > > I always run the jemboos installer script to install everything > (embassy included), and follow the Jemboss installation guide for OS > X. I also have it running fine on a dual-2.5GHz G5 running Panther > 10.3.9. > > When you update to Tiger, be sure to check the install option for the > new X11, and then, install the developers tools and the new X11 SDK. > And with Tiger, do NOT point the jemboss install script to Java 1.5, > stick with 1.4.2, or even 1.3. > > Michael > ____________________________________________ > Michael B. Black, Ph.D. > Molecular Biology Computing Support > ITC-ACHS, MSB rm.3013 > 982-4039 > mblack at virginia.edu > > Web support, see the Molecular Biology > section at: http://www.itc.virginia.edu/achs > ____________________________________________ > > > > On May 25, 2005, at 1:33 PM, Robin Colgrove wrote: > > > > > Hello all, > > > > After numerous attempts following suggestions on this list, I never > > have been able to get the X11 version of EMBOSS to install on my > > iBook under Mac OS X 10.3.8, but I installed and have been using > > the command line version without trouble (and using the GUI > > programs remotely with EMBOSS on a server and running the Mac X11 > > client locally). > > > > Next week I am going to upgrade to OSX 10.4 "Tiger", and was > > thinking of trying a full EMBOSS install again. I would be > > interested to hear from anyone who has done this (EMBOSS on Tiger) > > and any tips/advice. Also, it is not clear to me whether it would > > be best to uninstall everything and reinstall, or whether I could > > just install the X11 parts over an existing install. > > > > thanks > > > > Robin Colgrove > > Dept of Microbiology > > Harvard Medical School > > > > > > The Wellcome Trust Sanger Institute Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK From kvddrift at earthlink.net Thu May 26 10:32:24 2005 From: kvddrift at earthlink.net (Koen van der Drift) Date: Thu, 26 May 2005 06:32:24 -0400 Subject: [EMBOSS] Installation help In-Reply-To: <3502496E-6BAC-4571-B012-A00F8BE16D74@virginia.edu> References: <46609.129.111.174.49.1117036759.squirrel@biochem.uthscsa.edu> <70a549240c9938139675c7c16231a0b6@hms.harvard.edu> <3502496E-6BAC-4571-B012-A00F8BE16D74@virginia.edu> Message-ID: On May 25, 2005, at 7:47 PM, Michael Black wrote: > When you update to Tiger, be sure to check the install option for the > new X11, and then, install the developers tools and the new X11 SDK.? > And with Tiger, do NOT point the jemboss install script to Java 1.5, > stick with 1.4.2, or even 1.3. > Michael, What is the complete path to 1.4.2 on Tiger (on 10.3 it is "/System/Library/Frameworks/JavaVM.framework/Versions/1.4.2") ? I am the maintainer of the emboss package for fink and want to make sure that 1.5 is not used. thanks, - Koen. From mbb8n at virginia.edu Thu May 26 12:00:46 2005 From: mbb8n at virginia.edu (Michael Black) Date: Thu, 26 May 2005 08:00:46 -0400 Subject: [EMBOSS] Installation help In-Reply-To: References: <46609.129.111.174.49.1117036759.squirrel@biochem.uthscsa.edu> <70a549240c9938139675c7c16231a0b6@hms.harvard.edu> <3502496E-6BAC-4571-B012-A00F8BE16D74@virginia.edu> Message-ID: When I moved to Tiger on my powerbook, I just did a straightforward update, then applied the Java 1.5 update manually (since SU never saw it). The path to Java is still /System/Library/Frameworks/JavaVM.framework/Versions then there are the following version directories: lrwxr-xr-x 1 root wheel 5 Apr 30 14:51 1.3 -> 1.3.1 drwxr-xr-x 8 root wheel 272 Apr 30 14:51 1.3.1 lrwxr-xr-x 1 root wheel 5 Apr 30 14:51 1.4 -> 1.4.2 drwxr-xr-x 8 root wheel 272 Jan 26 15:22 1.4.2 lrwxr-xr-x 1 root wheel 5 May 12 11:15 1.5 -> 1.5.0 drwxr-xr-x 8 root wheel 272 May 12 11:15 1.5.0 drwxr-xr-x 6 root wheel 204 May 16 19:47 A lrwxr-xr-x 1 root wheel 1 Apr 30 14:51 Current -> A lrwxr-xr-x 1 root wheel 5 Apr 30 14:51 CurrentJDK - > 1.4.2 When I recompiled jemboss/EMBOSS (standalone installation) with the new developers tools, I used /System/Library/Frameworks/JavaVM.framework/Versions/1.4.2 I tried compiling with 1.5, but got all sorts of java errors when I tried to launch jemboss. Michael ____________________________________________ Michael B. Black, Ph.D. Molecular Biology Computing Support ITC-ACHS, MSB rm.3013 982-4039 mblack at virginia.edu Web support, see the Molecular Biology section at: http://www.itc.virginia.edu/achs ____________________________________________ On May 26, 2005, at 6:32 AM, Koen van der Drift wrote: > > On May 25, 2005, at 7:47 PM, Michael Black wrote: > > >> When you update to Tiger, be sure to check the install option for >> the new X11, and then, install the developers tools and the new >> X11 SDK. And with Tiger, do NOT point the jemboss install script >> to Java 1.5, stick with 1.4.2, or even 1.3. >> >> > > Michael, > > What is the complete path to 1.4.2 on Tiger (on 10.3 it is "/System/ > Library/Frameworks/JavaVM.framework/Versions/1.4.2") ? I am the > maintainer of the emboss package for fink and want to make sure > that 1.5 is not used. > > > thanks, > > - Koen. > > From Richard.Rothery at ualberta.ca Thu May 26 15:33:53 2005 From: Richard.Rothery at ualberta.ca (Richard Rothery) Date: Thu, 26 May 2005 09:33:53 -0600 Subject: [EMBOSS] EMBOSS database configurartion...... Message-ID: <000001c56208$52d9e800$5e068081@Nordegg> Hi All, How does one configuire EMBOSS to retrieve sequences directly from swissprot/trembl? Specifically what lines have to be added to the database configuration file? Something that links to the EXPASY site? The idea here is to use SEQRET to grab the sequences. I have no room on my system for the entire database, indexing etc... Hopefully, the answer to this one will be simple!! Thanks, Richard ############################################### CIHR Membrane Protein Research Group, Department of Biochemistry, University of Alberta, Edmonton T6G 2H7 Ph. (780) 492-2229 Fax. (780) 492-0886 ############################################### -------------- next part -------------- An HTML attachment was scrubbed... URL: From pmr at ebi.ac.uk Thu May 26 16:39:25 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 26 May 2005 17:39:25 +0100 Subject: [EMBOSS] EMBOSS database configurartion...... In-Reply-To: <000001c56208$52d9e800$5e068081@Nordegg> References: <000001c56208$52d9e800$5e068081@Nordegg> Message-ID: <4295FBBD.7040302@ebi.ac.uk> Richard Rothery wrote: > How does one configuire EMBOSS to retrieve sequences directly from > swissprot/trembl? Specifically what lines have to be added to the > database configuration file? Something that links to the EXPASY site? > The idea here is to use SEQRET to grab the sequences. I have no room on > my system for the entire database, indexing etc... Using the EBI SRS server ... depends on which database you would like: DB uniprot [ type: P format: swiss method: srswww dbalias: uniprot url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz" ] DB sptrembl [ type: P format: swiss method: srswww dbalias: sptrembl url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz" ] DB swissprot [ type: P format: swiss method: srswww dbalias: swissprot url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz" ] Using EXPASY's SRS server (in the USA): Note the spelling of the database alias with an underscore DB expasy [ type: P format: swiss method: srswww dbalias: swiss_prot url: "http://us.expasy.org/srs5bin/cgi-bin/wgetz" ] These will all search by ID and accession number > Hopefully, the answer to this one will be simple!! There will be many possible answers. These were just a few suggestions! regards, Peter Rice From stefanielager at fastmail.ca Fri May 27 06:06:50 2005 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Fri, 27 May 2005 06:06:50 +0000 (UTC) Subject: [EMBOSS] EMBOSS database configurartion...... In-Reply-To: <4295FBBD.7040302@ebi.ac.uk> Message-ID: <20050527060650.AB45A86163E@mail.interchange.ca> Using method: URL you can also retrive entries from Swissprot (or UniProt) from http://www.ebi.uniprot.org or via dbfetch http://www.ebi.ac.uk/cgi-bin/dbfetch Stefanie > Richard Rothery wrote: > >> How does one configuire EMBOSS to retrieve sequences directly from >> swissprot/trembl? Specifically what lines have to be added to the >> database configuration file? Something that links to the EXPASY site? >> The idea here is to use SEQRET to grab the sequences. I have no room >> on my system for the entire database, indexing etc... > > Using the EBI SRS server ... depends on which database you would like: > > DB uniprot [ > type: P > format: swiss > method: srswww > dbalias: uniprot > url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz" > ] > > DB sptrembl [ > type: P > format: swiss > method: srswww > dbalias: sptrembl > url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz" > ] > > DB swissprot [ > type: P > format: swiss > method: srswww > dbalias: swissprot > url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz" > ] > > Using EXPASY's SRS server (in the USA): > > Note the spelling of the database alias with an underscore > > DB expasy [ > type: P > format: swiss > method: srswww > dbalias: swiss_prot > url: "http://us.expasy.org/srs5bin/cgi-bin/wgetz" > ] > > These will all search by ID and accession number > > >> Hopefully, the answer to this one will be simple!! > > There will be many possible answers. These were just a few > suggestions! > > > regards, > > Peter Rice _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians