From ppetrov at mail.student.oulu.fi Mon Sep 5 15:42:26 2011 From: ppetrov at mail.student.oulu.fi (Petar Petrov) Date: Mon, 05 Sep 2011 22:42:26 +0300 Subject: [EMBOSS] EMBOSS and EMBASSY included in SlackBuilds.org Message-ID: <20110905224226.k8oyb5nzhwcs0g00@webmail.oulu.fi> Hi to all EMBOSS and EMBASSY have been included in the SlackBuilds.org repository: http://slackbuilds.org/repository/13.37/academic/EMBOSS/ http://slackbuilds.org/repository/13.37/academic/EMBASSY/ If you have any remarks regarding the applications descriptions, the SlackBuild scripts or the citing information, please let me know. I will highly appreciate any recommendations concerning the SlackBuild scripts. Many thanks for EMBOSS and the associated EMBASSY! Best wishes, Petar From ajb at ebi.ac.uk Tue Sep 6 04:52:42 2011 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Tue, 6 Sep 2011 09:52:42 +0100 (BST) Subject: [EMBOSS] EMBOSS and mEMBOSS bug-fix set 1-21 released Message-ID: <35573.82.26.12.214.1315299162.squirrel@imap04.ebi.ac.uk> New bug-fixes are available for EMBOSS-6.4.0 and, for Windows users, a new version of mEMBOSS is available. The bugs fixed include those recently fixed (12-21), listed below, and all those fixed by previous patches (1-11). 1) UNIX As usual, the most convenient way of applying the bug-fixes is to apply the patch file: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-21.gz to a freshly extracted copy of the EMBOSS-6.4.0.tar.gz source code and recompiling/installing. (see ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/README.patch for instructions on using 'patch'). Alternatively, you can individually copy the patched files from the ftp://emboss.open-bio.org/pub/EMBOSS/fixes/ directory if your system does not support 'patch'. 2) mEMBOSS The new version incorporates all new and previous bug-fixes. Uninstall your previous mEMBOSS installation and download and install the new setup file from: ftp://emboss.open-bio.org/pub/EMBOSS/windows/mEMBOSS-6.4.0.3-setup.exe Alan ----------------------------------------------------------------------- Fix 12. EMBOSS-6.4.0/nucleus/embgroup.c 18-Aug-2011: An internal string variable should be initialised as NULL. Fix 13. EMBOSS-6.4.0/ajax/core/ajseqread.c 18-Aug-2011: Reading protein GFF3 files ignored the EMBOSS type comment. This appears to be the only way to detect a protein GFF3 file. Fix 14. EMBOSS-6.4.0/emboss/data/Efeatures.gff3protein 18-Aug-2011: In writing GFF3 protein file, uses the current term name from the Sequence Ontology to clear errors from the GFF3 online validator. Fix 15. EMBOSS-6.4.0/ajax/core/ajfeatwrite.c 18-Aug-2011: When writing GFF3 format, tags names are explicitly converted to lower case as required by the GFF3 standard. This includes EC_number and /PCR_conditions in EMBL/GenBank/DDBJ and several RefseqP tags. The score is written using g format to represent very low values. Fix 16. EMBOSS-6.4.0/ajax/core/ajnexus.c EMBOSS-6.4.0/ajax/core/ajseqread.c 22-Aug-2011: When reading nexus data format with no taxlabels block the attempt to read the taxa (sequence names) from the matrix block failed. Fix 17. EMBOSS-6.4.0/ajax/ajaxdb/ajtextdb.c 22-Aug-2011: The SRS access method added a stray '+' character to the getz command line. Fix 18. EMBOSS-6.4.0/ajax/core/ajquery.c 25-Aug-2011: In some cases a query using a simple identifier could try to test an undefined "sv" field. Fix 19. EMBOSS-6.4.0/ajax/core/ajseqread.c 02-Sep-2011: Reading "raw" sequence format failed when piped from standard input. In release 6.4.0 "raw" format was redefined as a binary format to catch binary files that start with one or more sequence characters followed by a NULL character. This fix continues to check binary files, but has to drop the check for data piped through standard input which is read as text and cannot be reread as binary. Fix 20. EMBOSS-6.4.0/ajax/core/ajnam.c 02-Sep-2011: Complex database definitions with more than one type or format are allowed in 6.4.0 but caused an error message from showdb when the type and format were tested. Fix 21. EMBOSS-6.4.0/emboss/drfinddata.c EMBOSS-6.4.0/emboss/drfindformat.c EMBOSS-6.4.0/emboss/drfindid.c EMBOSS-6.4.0/emboss/drfindresource.c 02-Sep-2011: Running with -debug fails. Debug calls used obsolete datatype for data resource internals. Without -debug there was no problem. From sylvain.foisy at diploide.net Tue Sep 6 13:27:20 2011 From: sylvain.foisy at diploide.net (Sylvain Foisy Ph. D.) Date: Tue, 6 Sep 2011 13:27:20 -0400 Subject: [EMBOSS] Failure to build on Ubuntu 11.04 Message-ID: HI, I've build EMBOSS on numerous vertsion of Ubuntu before but this one got me stumped... I am testing an EMBOSS 6.4.0 build on an Ubuntu 11.04 VM under VirtualBox, pretty much as I have done before and I end up with an oddity (may be the problem) and a make failure. First the oddity: running the install-jemboss-server.sh script, I get this: ------------------------- WARNING ---------------------------- The script cannot find zlib installed under /usr or /usr/local Download zlib from http://www.info-zip.org/pub/infozip/zlib/ For details see the EMBOSS admin guide: http://emboss.sourceforge.net/admin/ To exit use Control C or press return to continue. -------------------------------------------------------------- This is weird because I know that zlibc, zlib1g and zlib1g-dev packages are present. Ok, I press return and the configure/make dance started. After a few minutes, make crashes with this message: ../ajax/core/.libs/libajax.so: undefined reference to `crypt' collect2: ld returned 1 exit status make[2]: *** [aaindexextract] Error 1 make[2]: Leaving directory `/opt/bio/sources/EMBOSS-6.4.0/emboss' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/opt/bio/sources/EMBOSS-6.4.0/emboss' make: *** [all-recursive] Error 1 Any clue on this? I couldn't find any lead looking at the mailing list archive... Best regards Sylvain From charles-listes-emboss at plessy.org Wed Sep 7 00:40:40 2011 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Wed, 7 Sep 2011 13:40:40 +0900 Subject: [EMBOSS] Failure to build on Ubuntu 11.04 In-Reply-To: References: Message-ID: <20110907044040.GD25495@merveille.plessy.net> Le Tue, Sep 06, 2011 at 01:27:20PM -0400, Sylvain Foisy Ph. D. a ?crit : > > ------------------------- WARNING ---------------------------- > > The script cannot find zlib installed under /usr > or /usr/local > > Download zlib from > http://www.info-zip.org/pub/infozip/zlib/ > > For details see the EMBOSS admin guide: > http://emboss.sourceforge.net/admin/ > > To exit use Control C or press return to continue. Dear Sylvain, perhaps you can try to pass the --enable-systemlibs option during configuration ? Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From ajb at ebi.ac.uk Wed Sep 7 07:04:56 2011 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Wed, 7 Sep 2011 12:04:56 +0100 (BST) Subject: [EMBOSS] Failure to build on Ubuntu 11.04 In-Reply-To: References: Message-ID: <47915.82.26.12.214.1315393496.squirrel@imap04.ebi.ac.uk> Hello Sylvain, Regarding the oddity: having had a look, the Ubuntu people have decided to put some libraries in different locations from most other linux distributions. I've modified the script which should now , at least, fix that problem. You can download it from: http://www.ebi.ac.uk/~ajb/test/install-jemboss-server.sh (you may need to "chmod 755" it after download). Wrt crypt: the above script works for me using PAM authentication (requires libpam0g-dev installation). I can't guarantee it'll work with other authentication methods on Ubuntu yet, given their library organisation, but feel free to test it and let me know. Before you do that though, please send me your jemboss/utils/install.record file (produced automatically after you ran the installation script - edit it to replace any sensitive info with 'x's first) so I can see what options you had chosen to give before the compilation failed (in order to try to reproduce the original failure). We do, however, recommend PAM authentication for servers on those distributions that support PAM. HTH Alan > HI, > > I've build EMBOSS on numerous vertsion of Ubuntu before but this one got > me stumped... I am testing an EMBOSS 6.4.0 build on an Ubuntu 11.04 VM > under VirtualBox, pretty much as I have done before and I end up with an > oddity (may be the problem) and a make failure. First the oddity: running > the install-jemboss-server.sh script, I get this: > > ------------------------- WARNING ---------------------------- > > The script cannot find zlib installed under /usr > or /usr/local > > Download zlib from > http://www.info-zip.org/pub/infozip/zlib/ > > For details see the EMBOSS admin guide: > http://emboss.sourceforge.net/admin/ > > To exit use Control C or press return to continue. > > -------------------------------------------------------------- > > This is weird because I know that zlibc, zlib1g and zlib1g-dev packages > are present. Ok, I press return and the configure/make dance started. > After a few minutes, make crashes with this message: > > ../ajax/core/.libs/libajax.so: undefined reference to `crypt' > collect2: ld returned 1 exit status > make[2]: *** [aaindexextract] Error 1 > make[2]: Leaving directory `/opt/bio/sources/EMBOSS-6.4.0/emboss' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory `/opt/bio/sources/EMBOSS-6.4.0/emboss' > make: *** [all-recursive] Error 1 > > > Any clue on this? I couldn't find any lead looking at the mailing list > archive... > > Best regards > > Sylvain > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From sylvain.foisy at diploide.net Wed Sep 7 15:32:50 2011 From: sylvain.foisy at diploide.net (Sylvain Foisy Ph. D.) Date: Wed, 7 Sep 2011 15:32:50 -0400 Subject: [EMBOSS] Failure to build on Ubuntu 11.04 In-Reply-To: <47915.82.26.12.214.1315393496.squirrel@imap04.ebi.ac.uk> References: <47915.82.26.12.214.1315393496.squirrel@imap04.ebi.ac.uk> Message-ID: <19413095-BDD6-4B5F-A098-A5AC97692F5B@diploide.net> Hi, On 2011-09-07, at 7:04 AM, ajb at ebi.ac.uk wrote: > Regarding the oddity: having had a look, the Ubuntu people have > decided to put some libraries in different locations from > most other linux distributions. I've modified the script > which should now , at least, fix that problem. You can download it from: > > http://www.ebi.ac.uk/~ajb/test/install-jemboss-server.sh > > (you may need to "chmod 755" it after download). Ah, Linux distros... I tried the new script, with default choices, with a clean d/l of EMBOSS and EMBASSY apps and I got this: ajjava.c:122:31: fatal error: security/pam_appl.h: No such file or directory compilation terminated. make[3]: *** [ajjava.lo] Error 1 make[3]: Leaving directory `/opt/bio/sources/EMBOSS-6.4.0/ajax/core' make[2]: *** [all] Error 2 make[2]: Leaving directory `/opt/bio/sources/EMBOSS-6.4.0/ajax/core' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/opt/bio/sources/EMBOSS-6.4.0/ajax' make: *** [all-recursive] Error 1 Let me guess: % apt-get install libpam0g-dev Right? Must be because compilation did work a-ok with the script after this install. > Wrt crypt: the above script works for me using PAM authentication > (requires libpam0g-dev installation). I can't guarantee it'll > work with other authentication methods on Ubuntu yet, given > their library organisation, but feel free to test it and let me > know. Before you do that though, please send me your > jemboss/utils/install.record file (produced automatically after you ran > the installation script - edit it to replace any sensitive info > with 'x's first) so I can see what options you had chosen to > give before the compilation failed (in order to try to > reproduce the original failure). We do, however, recommend PAM > authentication for servers on those distributions that > support PAM. I had selected shadow, which might explain this error. I actually never use jemboss in a client-server setup but rather as a local standalone resource on the server for the users to use locally via the Xfce4 GUI. BTW, the script is not using axis2c yet? It only recognized axis-1_4. Thanks for the help Sylvain From ajb at ebi.ac.uk Thu Sep 8 05:38:12 2011 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Thu, 8 Sep 2011 10:38:12 +0100 (BST) Subject: [EMBOSS] Failure to build on Ubuntu 11.04 In-Reply-To: <19413095-BDD6-4B5F-A098-A5AC97692F5B@diploide.net> References: <47915.82.26.12.214.1315393496.squirrel@imap04.ebi.ac.uk> <19413095-BDD6-4B5F-A098-A5AC97692F5B@diploide.net> Message-ID: <58688.82.26.12.214.1315474692.squirrel@imap04.ebi.ac.uk> Hi Sylvain, > I had selected shadow, which might explain this error. I actually never > use jemboss in a client-server setup but rather as a local standalone > resource on the server for the users to use locally via the Xfce4 GUI. > BTW, the script is not using axis2c yet? It only recognized axis-1_4. The 'shadow' selection is a bug which could be worked around for now, if necessary, by typing: export LDFLAGS=-lcrypt (setenv LDFLAGS -lcrypt) before invoking the script. It'll be fixed in the next release. However, as mentioned, PAM is better anyway and doesn't require doing so. I'm not sure from your message whether you're aware that you don't need to invoke the server script if you just want a simple standalone Jemboss for your users. Any EMBOSS installation using "make install" will create a script in the 'bin' directory called 'runJemboss.csh'. If users invoke that script (possibly via a symlink of your choice) then, as long as you have java in your PATH, it will fire-up a pre-configured standalone jemboss. The results of any applications will be stored in a jemboss subdirectory in a users home directory. As far as I'm aware axis2c isn't used by Jemboss yet, though it can be optionally configured into EMBOSS itself as a means of accessing some servers. ATB Alan From pwhitley at scmmlab.com Wed Sep 28 15:47:35 2011 From: pwhitley at scmmlab.com (Penn Whitley) Date: Wed, 28 Sep 2011 12:47:35 -0700 Subject: [EMBOSS] EMBOSS:complex Message-ID: <852F3CE51CA0E54EAF06FEE63291BA58B43600@SQNMEP4.sequenom.com> Hello, I have recently installed v6.4.0. I am trying to use the complex program for estimating linguistic complexity of DNA but cannot seem to find the program in my release. I was able to find the documentation though. Does anyone know if complex is no longer part of the release or if any special flags are required during the install. Thanks in advance, Penn From pmr at ebi.ac.uk Thu Sep 29 04:11:51 2011 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 29 Sep 2011 09:11:51 +0100 Subject: [EMBOSS] EMBOSS:complex In-Reply-To: <852F3CE51CA0E54EAF06FEE63291BA58B43600@SQNMEP4.sequenom.com> References: <852F3CE51CA0E54EAF06FEE63291BA58B43600@SQNMEP4.sequenom.com> Message-ID: <4E842847.6040306@ebi.ac.uk> Dear Penn, On 28/09/2011 20:47, Penn Whitley wrote: > I have recently installed v6.4.0. I am trying to use the complex > program for estimating linguistic complexity of DNA but cannot seem to > find the program in my release. I was able to find the documentation > though. Does anyone know if complex is no longer part of the release or > if any special flags are required during the install. Both ... no longer part of the release, and special flags required. Complex is no longer maintained. It was an early addition to the package before release 1.0.0 and has not been updated since then. The program is still there - you can compile it using "make check" and run it from the emboss source directory. If this program is useful to anyone then we will reinstate it in the main package. Do please let us know what you think of it. regards, Peter Rice EMBOSS Team From ebs15242 at creighton.edu Fri Sep 30 14:22:00 2011 From: ebs15242 at creighton.edu (Ed Siefker) Date: Fri, 30 Sep 2011 13:22:00 -0500 Subject: [EMBOSS] Remote Genbank from NCBI? Message-ID: <4E8608C8.3090502@creighton.edu> Is there a way to access NCBI Genbank remotely? My emboss.default contains the following: DB tgb [ type: N method: srswww format: genbank url: "http://cbr-rbc.nrc-cnrc.gc.ca/srs6bin/cgi-bin/wgetz" dbalias: genbankrelease fields: "sv des org key" comment: "Genbank IDs" ] However that server does not exist. I've looked on the NCBI website for alternatives, but all I can find is the ftp site. I've also read the EMBOSS admin guide. The examples there use infobiogen.fr, which is also closed. So what do people do for genbank access? I'd prefer to avoid setting up a local database myself if I can. Is there a list of genbank mirrors around somewhere? From ppetrov at mail.student.oulu.fi Mon Sep 5 19:42:26 2011 From: ppetrov at mail.student.oulu.fi (Petar Petrov) Date: Mon, 05 Sep 2011 22:42:26 +0300 Subject: [EMBOSS] EMBOSS and EMBASSY included in SlackBuilds.org Message-ID: <20110905224226.k8oyb5nzhwcs0g00@webmail.oulu.fi> Hi to all EMBOSS and EMBASSY have been included in the SlackBuilds.org repository: http://slackbuilds.org/repository/13.37/academic/EMBOSS/ http://slackbuilds.org/repository/13.37/academic/EMBASSY/ If you have any remarks regarding the applications descriptions, the SlackBuild scripts or the citing information, please let me know. I will highly appreciate any recommendations concerning the SlackBuild scripts. Many thanks for EMBOSS and the associated EMBASSY! Best wishes, Petar From ajb at ebi.ac.uk Tue Sep 6 08:52:42 2011 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Tue, 6 Sep 2011 09:52:42 +0100 (BST) Subject: [EMBOSS] EMBOSS and mEMBOSS bug-fix set 1-21 released Message-ID: <35573.82.26.12.214.1315299162.squirrel@imap04.ebi.ac.uk> New bug-fixes are available for EMBOSS-6.4.0 and, for Windows users, a new version of mEMBOSS is available. The bugs fixed include those recently fixed (12-21), listed below, and all those fixed by previous patches (1-11). 1) UNIX As usual, the most convenient way of applying the bug-fixes is to apply the patch file: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-21.gz to a freshly extracted copy of the EMBOSS-6.4.0.tar.gz source code and recompiling/installing. (see ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/README.patch for instructions on using 'patch'). Alternatively, you can individually copy the patched files from the ftp://emboss.open-bio.org/pub/EMBOSS/fixes/ directory if your system does not support 'patch'. 2) mEMBOSS The new version incorporates all new and previous bug-fixes. Uninstall your previous mEMBOSS installation and download and install the new setup file from: ftp://emboss.open-bio.org/pub/EMBOSS/windows/mEMBOSS-6.4.0.3-setup.exe Alan ----------------------------------------------------------------------- Fix 12. EMBOSS-6.4.0/nucleus/embgroup.c 18-Aug-2011: An internal string variable should be initialised as NULL. Fix 13. EMBOSS-6.4.0/ajax/core/ajseqread.c 18-Aug-2011: Reading protein GFF3 files ignored the EMBOSS type comment. This appears to be the only way to detect a protein GFF3 file. Fix 14. EMBOSS-6.4.0/emboss/data/Efeatures.gff3protein 18-Aug-2011: In writing GFF3 protein file, uses the current term name from the Sequence Ontology to clear errors from the GFF3 online validator. Fix 15. EMBOSS-6.4.0/ajax/core/ajfeatwrite.c 18-Aug-2011: When writing GFF3 format, tags names are explicitly converted to lower case as required by the GFF3 standard. This includes EC_number and /PCR_conditions in EMBL/GenBank/DDBJ and several RefseqP tags. The score is written using g format to represent very low values. Fix 16. EMBOSS-6.4.0/ajax/core/ajnexus.c EMBOSS-6.4.0/ajax/core/ajseqread.c 22-Aug-2011: When reading nexus data format with no taxlabels block the attempt to read the taxa (sequence names) from the matrix block failed. Fix 17. EMBOSS-6.4.0/ajax/ajaxdb/ajtextdb.c 22-Aug-2011: The SRS access method added a stray '+' character to the getz command line. Fix 18. EMBOSS-6.4.0/ajax/core/ajquery.c 25-Aug-2011: In some cases a query using a simple identifier could try to test an undefined "sv" field. Fix 19. EMBOSS-6.4.0/ajax/core/ajseqread.c 02-Sep-2011: Reading "raw" sequence format failed when piped from standard input. In release 6.4.0 "raw" format was redefined as a binary format to catch binary files that start with one or more sequence characters followed by a NULL character. This fix continues to check binary files, but has to drop the check for data piped through standard input which is read as text and cannot be reread as binary. Fix 20. EMBOSS-6.4.0/ajax/core/ajnam.c 02-Sep-2011: Complex database definitions with more than one type or format are allowed in 6.4.0 but caused an error message from showdb when the type and format were tested. Fix 21. EMBOSS-6.4.0/emboss/drfinddata.c EMBOSS-6.4.0/emboss/drfindformat.c EMBOSS-6.4.0/emboss/drfindid.c EMBOSS-6.4.0/emboss/drfindresource.c 02-Sep-2011: Running with -debug fails. Debug calls used obsolete datatype for data resource internals. Without -debug there was no problem. From sylvain.foisy at diploide.net Tue Sep 6 17:27:20 2011 From: sylvain.foisy at diploide.net (Sylvain Foisy Ph. D.) Date: Tue, 6 Sep 2011 13:27:20 -0400 Subject: [EMBOSS] Failure to build on Ubuntu 11.04 Message-ID: HI, I've build EMBOSS on numerous vertsion of Ubuntu before but this one got me stumped... I am testing an EMBOSS 6.4.0 build on an Ubuntu 11.04 VM under VirtualBox, pretty much as I have done before and I end up with an oddity (may be the problem) and a make failure. First the oddity: running the install-jemboss-server.sh script, I get this: ------------------------- WARNING ---------------------------- The script cannot find zlib installed under /usr or /usr/local Download zlib from http://www.info-zip.org/pub/infozip/zlib/ For details see the EMBOSS admin guide: http://emboss.sourceforge.net/admin/ To exit use Control C or press return to continue. -------------------------------------------------------------- This is weird because I know that zlibc, zlib1g and zlib1g-dev packages are present. Ok, I press return and the configure/make dance started. After a few minutes, make crashes with this message: ../ajax/core/.libs/libajax.so: undefined reference to `crypt' collect2: ld returned 1 exit status make[2]: *** [aaindexextract] Error 1 make[2]: Leaving directory `/opt/bio/sources/EMBOSS-6.4.0/emboss' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/opt/bio/sources/EMBOSS-6.4.0/emboss' make: *** [all-recursive] Error 1 Any clue on this? I couldn't find any lead looking at the mailing list archive... Best regards Sylvain From charles-listes-emboss at plessy.org Wed Sep 7 04:40:40 2011 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Wed, 7 Sep 2011 13:40:40 +0900 Subject: [EMBOSS] Failure to build on Ubuntu 11.04 In-Reply-To: References: Message-ID: <20110907044040.GD25495@merveille.plessy.net> Le Tue, Sep 06, 2011 at 01:27:20PM -0400, Sylvain Foisy Ph. D. a ?crit : > > ------------------------- WARNING ---------------------------- > > The script cannot find zlib installed under /usr > or /usr/local > > Download zlib from > http://www.info-zip.org/pub/infozip/zlib/ > > For details see the EMBOSS admin guide: > http://emboss.sourceforge.net/admin/ > > To exit use Control C or press return to continue. Dear Sylvain, perhaps you can try to pass the --enable-systemlibs option during configuration ? Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From ajb at ebi.ac.uk Wed Sep 7 11:04:56 2011 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Wed, 7 Sep 2011 12:04:56 +0100 (BST) Subject: [EMBOSS] Failure to build on Ubuntu 11.04 In-Reply-To: References: Message-ID: <47915.82.26.12.214.1315393496.squirrel@imap04.ebi.ac.uk> Hello Sylvain, Regarding the oddity: having had a look, the Ubuntu people have decided to put some libraries in different locations from most other linux distributions. I've modified the script which should now , at least, fix that problem. You can download it from: http://www.ebi.ac.uk/~ajb/test/install-jemboss-server.sh (you may need to "chmod 755" it after download). Wrt crypt: the above script works for me using PAM authentication (requires libpam0g-dev installation). I can't guarantee it'll work with other authentication methods on Ubuntu yet, given their library organisation, but feel free to test it and let me know. Before you do that though, please send me your jemboss/utils/install.record file (produced automatically after you ran the installation script - edit it to replace any sensitive info with 'x's first) so I can see what options you had chosen to give before the compilation failed (in order to try to reproduce the original failure). We do, however, recommend PAM authentication for servers on those distributions that support PAM. HTH Alan > HI, > > I've build EMBOSS on numerous vertsion of Ubuntu before but this one got > me stumped... I am testing an EMBOSS 6.4.0 build on an Ubuntu 11.04 VM > under VirtualBox, pretty much as I have done before and I end up with an > oddity (may be the problem) and a make failure. First the oddity: running > the install-jemboss-server.sh script, I get this: > > ------------------------- WARNING ---------------------------- > > The script cannot find zlib installed under /usr > or /usr/local > > Download zlib from > http://www.info-zip.org/pub/infozip/zlib/ > > For details see the EMBOSS admin guide: > http://emboss.sourceforge.net/admin/ > > To exit use Control C or press return to continue. > > -------------------------------------------------------------- > > This is weird because I know that zlibc, zlib1g and zlib1g-dev packages > are present. Ok, I press return and the configure/make dance started. > After a few minutes, make crashes with this message: > > ../ajax/core/.libs/libajax.so: undefined reference to `crypt' > collect2: ld returned 1 exit status > make[2]: *** [aaindexextract] Error 1 > make[2]: Leaving directory `/opt/bio/sources/EMBOSS-6.4.0/emboss' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory `/opt/bio/sources/EMBOSS-6.4.0/emboss' > make: *** [all-recursive] Error 1 > > > Any clue on this? I couldn't find any lead looking at the mailing list > archive... > > Best regards > > Sylvain > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From sylvain.foisy at diploide.net Wed Sep 7 19:32:50 2011 From: sylvain.foisy at diploide.net (Sylvain Foisy Ph. D.) Date: Wed, 7 Sep 2011 15:32:50 -0400 Subject: [EMBOSS] Failure to build on Ubuntu 11.04 In-Reply-To: <47915.82.26.12.214.1315393496.squirrel@imap04.ebi.ac.uk> References: <47915.82.26.12.214.1315393496.squirrel@imap04.ebi.ac.uk> Message-ID: <19413095-BDD6-4B5F-A098-A5AC97692F5B@diploide.net> Hi, On 2011-09-07, at 7:04 AM, ajb at ebi.ac.uk wrote: > Regarding the oddity: having had a look, the Ubuntu people have > decided to put some libraries in different locations from > most other linux distributions. I've modified the script > which should now , at least, fix that problem. You can download it from: > > http://www.ebi.ac.uk/~ajb/test/install-jemboss-server.sh > > (you may need to "chmod 755" it after download). Ah, Linux distros... I tried the new script, with default choices, with a clean d/l of EMBOSS and EMBASSY apps and I got this: ajjava.c:122:31: fatal error: security/pam_appl.h: No such file or directory compilation terminated. make[3]: *** [ajjava.lo] Error 1 make[3]: Leaving directory `/opt/bio/sources/EMBOSS-6.4.0/ajax/core' make[2]: *** [all] Error 2 make[2]: Leaving directory `/opt/bio/sources/EMBOSS-6.4.0/ajax/core' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/opt/bio/sources/EMBOSS-6.4.0/ajax' make: *** [all-recursive] Error 1 Let me guess: % apt-get install libpam0g-dev Right? Must be because compilation did work a-ok with the script after this install. > Wrt crypt: the above script works for me using PAM authentication > (requires libpam0g-dev installation). I can't guarantee it'll > work with other authentication methods on Ubuntu yet, given > their library organisation, but feel free to test it and let me > know. Before you do that though, please send me your > jemboss/utils/install.record file (produced automatically after you ran > the installation script - edit it to replace any sensitive info > with 'x's first) so I can see what options you had chosen to > give before the compilation failed (in order to try to > reproduce the original failure). We do, however, recommend PAM > authentication for servers on those distributions that > support PAM. I had selected shadow, which might explain this error. I actually never use jemboss in a client-server setup but rather as a local standalone resource on the server for the users to use locally via the Xfce4 GUI. BTW, the script is not using axis2c yet? It only recognized axis-1_4. Thanks for the help Sylvain From ajb at ebi.ac.uk Thu Sep 8 09:38:12 2011 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Thu, 8 Sep 2011 10:38:12 +0100 (BST) Subject: [EMBOSS] Failure to build on Ubuntu 11.04 In-Reply-To: <19413095-BDD6-4B5F-A098-A5AC97692F5B@diploide.net> References: <47915.82.26.12.214.1315393496.squirrel@imap04.ebi.ac.uk> <19413095-BDD6-4B5F-A098-A5AC97692F5B@diploide.net> Message-ID: <58688.82.26.12.214.1315474692.squirrel@imap04.ebi.ac.uk> Hi Sylvain, > I had selected shadow, which might explain this error. I actually never > use jemboss in a client-server setup but rather as a local standalone > resource on the server for the users to use locally via the Xfce4 GUI. > BTW, the script is not using axis2c yet? It only recognized axis-1_4. The 'shadow' selection is a bug which could be worked around for now, if necessary, by typing: export LDFLAGS=-lcrypt (setenv LDFLAGS -lcrypt) before invoking the script. It'll be fixed in the next release. However, as mentioned, PAM is better anyway and doesn't require doing so. I'm not sure from your message whether you're aware that you don't need to invoke the server script if you just want a simple standalone Jemboss for your users. Any EMBOSS installation using "make install" will create a script in the 'bin' directory called 'runJemboss.csh'. If users invoke that script (possibly via a symlink of your choice) then, as long as you have java in your PATH, it will fire-up a pre-configured standalone jemboss. The results of any applications will be stored in a jemboss subdirectory in a users home directory. As far as I'm aware axis2c isn't used by Jemboss yet, though it can be optionally configured into EMBOSS itself as a means of accessing some servers. ATB Alan From pwhitley at scmmlab.com Wed Sep 28 19:47:35 2011 From: pwhitley at scmmlab.com (Penn Whitley) Date: Wed, 28 Sep 2011 12:47:35 -0700 Subject: [EMBOSS] EMBOSS:complex Message-ID: <852F3CE51CA0E54EAF06FEE63291BA58B43600@SQNMEP4.sequenom.com> Hello, I have recently installed v6.4.0. I am trying to use the complex program for estimating linguistic complexity of DNA but cannot seem to find the program in my release. I was able to find the documentation though. Does anyone know if complex is no longer part of the release or if any special flags are required during the install. Thanks in advance, Penn From pmr at ebi.ac.uk Thu Sep 29 08:11:51 2011 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 29 Sep 2011 09:11:51 +0100 Subject: [EMBOSS] EMBOSS:complex In-Reply-To: <852F3CE51CA0E54EAF06FEE63291BA58B43600@SQNMEP4.sequenom.com> References: <852F3CE51CA0E54EAF06FEE63291BA58B43600@SQNMEP4.sequenom.com> Message-ID: <4E842847.6040306@ebi.ac.uk> Dear Penn, On 28/09/2011 20:47, Penn Whitley wrote: > I have recently installed v6.4.0. I am trying to use the complex > program for estimating linguistic complexity of DNA but cannot seem to > find the program in my release. I was able to find the documentation > though. Does anyone know if complex is no longer part of the release or > if any special flags are required during the install. Both ... no longer part of the release, and special flags required. Complex is no longer maintained. It was an early addition to the package before release 1.0.0 and has not been updated since then. The program is still there - you can compile it using "make check" and run it from the emboss source directory. If this program is useful to anyone then we will reinstate it in the main package. Do please let us know what you think of it. regards, Peter Rice EMBOSS Team From ebs15242 at creighton.edu Fri Sep 30 18:22:00 2011 From: ebs15242 at creighton.edu (Ed Siefker) Date: Fri, 30 Sep 2011 13:22:00 -0500 Subject: [EMBOSS] Remote Genbank from NCBI? Message-ID: <4E8608C8.3090502@creighton.edu> Is there a way to access NCBI Genbank remotely? My emboss.default contains the following: DB tgb [ type: N method: srswww format: genbank url: "http://cbr-rbc.nrc-cnrc.gc.ca/srs6bin/cgi-bin/wgetz" dbalias: genbankrelease fields: "sv des org key" comment: "Genbank IDs" ] However that server does not exist. I've looked on the NCBI website for alternatives, but all I can find is the ftp site. I've also read the EMBOSS admin guide. The examples there use infobiogen.fr, which is also closed. So what do people do for genbank access? I'd prefer to avoid setting up a local database myself if I can. Is there a list of genbank mirrors around somewhere?