From ableasby at hgmp.mrc.ac.uk Thu Jul 15 13:58:49 2004 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Thu, 15 Jul 2004 18:58:49 +0100 (BST) Subject: [EMBOSS] EMBOSS 2.9.0 released Message-ID: <200407151758.i6FHwnkW007992@bromine.hgmp.mrc.ac.uk> This email announces the release of EMBOSS 2.9.0; the traditional St Swithin's Day release prior to the ISMB conference. Many of the EMBOSS developers will be at ISMB. There will be an EMBOSS talk at BOSC, three related ISMB demonstrations (EMBOSS, JEMBOSS and Taverna) and we'll be present at the poster session. We hope to see you there. EMBOSS 2.9.0 can be downloaded via the new web site (emboss.sf.net) which we encourage people to start using. At present the download will be directed to the RFCGR ftp server; this will be changed. The old web site (www.rfcgr.mrc.ac.uk/Software/EMBOSS) will be removed within the year. Please note that the emboss.org domain has never been owned by the EMBOSS core developers so we have no control over any popups appearing on that site. As usual the changes appear in the ChangeLog file. A major feature of this release is extensive modifications to ACD and the libraries as part of the development of an EMBOSS ontology. This is to allow future provision of workflow analysis. The EMBASSY packages can now be compiled and linked against an installed version of EMBOSS. There is no need to retain the EMBOSS sources. This can be done from any directory. You just need to provide an appropriate --prefix= option to the configure command. The only exception is if you have installed EMBOSS in /usr/local/bin and associated directories. In this one case you must give the --enable-localforce option to your EMBASSY configure command as well. This does not apply to, for example, installations into /usr/local/emboss or any other directory hierarchy under /usr/local (the --prefix= option is enough). Older downloads of the EMBASSY packages will not work with 2.9.0; you should download them again. The decision of the MRC to close the RFCGR (see appended URL) has delayed the completion of several improvements (e.g. indexing, the new graphics library and the ACD ontology). We hope to get these out in the next release. We are, however, still seeking alternative sources of funding so it would therefore be unwise for us to give any firm assurances. Alan For the official MRC announcement of the closure of the RFCGR see: http://www.mrc.ac.uk/index/public-interest/public-council_meetings/ public-council_meetings_2003-04/public-council_meetings_31_mar04/ public-council_meeting_31_mar04_note.htm From hegedus at biomembrane.hu Thu Jul 15 14:31:11 2004 From: hegedus at biomembrane.hu (Tamas Hegedus) Date: Thu, 15 Jul 2004 20:31:11 +0200 (CEST) Subject: [EMBOSS] ModBioSQL release 0.12 Message-ID: Dear All, during my work I had to use RDBMS and EMBOSS. I collected my scripts and experiments into a package called Modular BioSQL, which has different features: -- Modular RDB realization of different biological databases allows fine-tuning with increased performance. -- Storing result sets in RDBMS allows more accurate, more comfortable analysis using SQL. -- User interaction with the RDBMS (installation, loading up and querying data) does not need programming skills. -- Light weight RDB interaction with analysis packages (only EMBOSS is implemented). -- Optimalized loading of flat files into the RDBMS. -- Using 'fixed value arrays' (*_ref tables) results in both smaller data size (smaller than the flat file) and smaller index size increasing the performance (theoretically both the uploading and querying performance). -- Relatively easily extendable to implement and handle databases other than the currently realized. You may think I suggest Modular BioSQL as a replacement of BioSQL. I do not think so! For details, please visit my web site, and send comments and suggestions: http://www.biomembrane.hu/~hegedus/modbiosql/ Best regards, Tamas -- Tam?s Heged?s, Research Associate | http://www.biomembrane.hu Membrane Research Group of | mailto:hegedus at biomembrane.hu Hungarian Academy of Sciences | tel: 36-1-3724317 H-1113 Budapest Dioszegi u 64, HUNGARY | fax: 36-1-3724353 From rsucgang at bcm.tmc.edu Thu Jul 15 18:32:40 2004 From: rsucgang at bcm.tmc.edu (richard sucgang phd) Date: Thu, 15 Jul 2004 17:32:40 -0500 Subject: [EMBOSS] sirna module In-Reply-To: <200407151758.i6FHwnkW007992@bromine.hgmp.mrc.ac.uk> References: <200407151758.i6FHwnkW007992@bromine.hgmp.mrc.ac.uk> Message-ID: Congratulations on the release of EMBOSS 2.9 I have been trying to use the sirna design program in EMBOSS, but have been getting a cryptic bus error message as it dies. I thought this may have been fixed in the newest version, but after compiling and installing, I get the same error. I am using MacOS X 10.3.4, with gobs of RAM, and a straightforward FASTA file. Any ideas as to what's going on? Thanks. -- Richard Sucgang, PhD (713) 798 7657 http://www.dictygenome.org/ From David.Bauer at SCHERING.DE Fri Jul 16 02:58:46 2004 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Fri, 16 Jul 2004 08:58:46 +0200 Subject: Antwort: [EMBOSS] sirna module Message-ID: This seems to be specific to MacOS X. I just updated to 2.9 on FreeBSD 4.9 and sirna is OK. (I also had no problems with sirna in 2.8, on Solaris and FreeBSD). David. richard sucgang phd Kopie: Gesendet von: Thema: [EMBOSS] sirna module owner-emboss at hgm p.mrc.ac.uk 16.07.2004 00:32 Congratulations on the release of EMBOSS 2.9 I have been trying to use the sirna design program in EMBOSS, but have been getting a cryptic bus error message as it dies. I thought this may have been fixed in the newest version, but after compiling and installing, I get the same error. I am using MacOS X 10.3.4, with gobs of RAM, and a straightforward FASTA file. Any ideas as to what's going on? Thanks. -- Richard Sucgang, PhD (713) 798 7657 http://www.dictygenome.org/ From d.gatherer at vir.gla.ac.uk Fri Jul 16 08:29:05 2004 From: d.gatherer at vir.gla.ac.uk (Derek Gatherer) Date: Fri, 16 Jul 2004 13:29:05 +0100 Subject: [EMBOSS] EMBOSS 2.9.0 released In-Reply-To: <200407151758.i6FHwnkW007992@bromine.hgmp.mrc.ac.uk> Message-ID: <5.2.1.1.1.20040716132757.00b160d0@udcf.gla.ac.uk> Hi Will cvs still be usable? cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/emboss login or does that have to be pointed at emboss.sf.net too? thanks Derek At 18:58 15/07/2004 +0100, Alan Bleasby wrote: >This email announces the release of EMBOSS 2.9.0; the traditional St >Swithin's Day release prior to the ISMB conference. Many of the EMBOSS >developers will be at ISMB. There will be an EMBOSS talk at BOSC, >three related ISMB demonstrations (EMBOSS, JEMBOSS and Taverna) and >we'll be present at the poster session. We hope to see you there. > >EMBOSS 2.9.0 can be downloaded via the new web site (emboss.sf.net) >which we encourage people to start using. At present the download will >be directed to the RFCGR ftp server; this will be changed. The old web >site (www.rfcgr.mrc.ac.uk/Software/EMBOSS) will be removed within the >year. Please note that the emboss.org domain has never been owned by >the EMBOSS core developers so we have no control over any popups >appearing on that site. > >As usual the changes appear in the ChangeLog file. A >major feature of this release is extensive modifications to ACD and >the libraries as part of the development of an EMBOSS ontology. This >is to allow future provision of workflow analysis. > >The EMBASSY packages can now be compiled and linked against an >installed version of EMBOSS. There is no need to retain the EMBOSS >sources. This can be done from any directory. You just need to provide >an appropriate --prefix= option to the configure command. The only >exception is if you have installed EMBOSS in /usr/local/bin and >associated directories. In this one case you must give the >--enable-localforce option to your EMBASSY configure command as >well. This does not apply to, for example, installations into >/usr/local/emboss or any other directory hierarchy under /usr/local >(the --prefix= option is enough). Older downloads of the EMBASSY >packages will not work with 2.9.0; you should download them again. > >The decision of the MRC to close the RFCGR (see appended URL) has >delayed the completion of several improvements (e.g. indexing, the new >graphics library and the ACD ontology). We hope to get these out in >the next release. We are, however, still seeking alternative sources >of funding so it would therefore be unwise for us to give any firm >assurances. > >Alan > >For the official MRC announcement of the closure of the RFCGR see: >http://www.mrc.ac.uk/index/public-interest/public-council_meetings/ >public-council_meetings_2003-04/public-council_meetings_31_mar04/ >public-council_meeting_31_mar04_note.htm _________________________ Derek Gatherer Ph.D. Cert.Ed. Computer Officer Institute of Virology Church St. Glasgow G11 5JR Phone: +44 141 330 6268 Fax: +44 141 337 2236 Email: d.gatherer at vir.gla.ac.uk Website: http://www.vir.gla.ac.uk From ableasby at hgmp.mrc.ac.uk Fri Jul 16 08:43:54 2004 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Fri, 16 Jul 2004 13:43:54 +0100 (BST) Subject: [EMBOSS] EMBOSS 2.9.0 released Message-ID: <200407161243.i6GChsKN022768@bromine.hgmp.mrc.ac.uk> Hello Derek, CVS will indeed still be usable from open-bio.org. There is no immediate intention to put a cvs server on sourceforge. Alan From pmr at ebi.ac.uk Fri Jul 16 08:43:56 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 16 Jul 2004 13:43:56 +0100 Subject: [EMBOSS] EMBOSS 2.9.0 released In-Reply-To: <5.2.1.1.1.20040716132757.00b160d0@udcf.gla.ac.uk> References: <5.2.1.1.1.20040716132757.00b160d0@udcf.gla.ac.uk> Message-ID: <40F7CD8C.6060107@ebi.ac.uk> Derek Gatherer wrote: > Will cvs still be usable? > > cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/emboss login > > or does that have to be pointed at emboss.sf.net too? We will be keeping the present CVS. Open Bio has been a good host, so we see no need to relocate CVS to Sourceforge. We relocated once before (in July 2000, from Sanger to open-bio) and would prefer not to move again. We will have to relocate a few things that are still at RFCGR: * The FTP server (that's where ftp.uk.embnet.org is) * The mailing list archives * The EFUNC and EDATA SRS databases (they can move to EBI) We aim to mirror everything ASAP in their new homes. The emboss.sourceforge.net website already has most of the content of the RFCGR (www.emboss.org) website. regards, Peter Rice From Bent.Terp at biosci.ki.se Fri Jul 16 09:08:16 2004 From: Bent.Terp at biosci.ki.se (Bent Terp) Date: Fri, 16 Jul 2004 15:08:16 +0200 Subject: [EMBOSS] Jemboss in local mode Message-ID: <1089983296.10815.64.camel@latte.biosci.ki.se> Hi all! I've been working a bit on producing RPM's of EMBOSS and friends, but still have a problem: When I launch jemboss in local mode, no window gets created but lots of cpu-time consumed. Are there any debug options that will reveal more? I've attached the launch script and jemboss.properties in case that helps. -- MVH / With kind regards, Bent Terp System Administrator Bioinformatics and Expression Analysis Core Facility Karolinska Institute, Department of Biosciences H?lsovagen 7-9, 141 57 Huddinge, Sweden -------------- next part -------------- A non-text attachment was scrubbed... Name: jemboss Type: text/x-sh Size: 1788 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss/attachments/20040716/63292d8e/attachment.bin -------------- next part -------------- user.auth=false jemboss.server=false plplot=/usr/share/EMBOSS/ embossData=/usr/share/EMBOSS/data/ embossBin=/usr/bin/ embossPath=/usr/bin:/bin:/packages/clustal/:/packages/primer3/bin:/data/jobqueue/bin/:/usr/ucb/ acdDirToParse=/usr/share/EMBOSS/acd/ embossURL=http://www.uk.embnet.org/Software/EMBOSS/Apps/ From yezq at mail.cbi.pku.edu.cn Tue Jul 20 06:10:43 2004 From: yezq at mail.cbi.pku.edu.cn (Zhiqiang Ye) Date: Tue, 20 Jul 2004 18:10:43 +0800 Subject: [EMBOSS] seqret problem? Message-ID: <200407201006.i6KA66i1014029@mail.cbi.pku.edu.cn> hi all?? I find that if there is a semicolon in the description line, seqret works wrong. [yezq at pro]$ more test >P1;Z1BPC2 MELTSTRKKANAITSSILNR IAIRGQRKVA DALGINESQI SRWKGDFIPK MGMLLAVLEW GVEDEELAEL AKKVAHLLTK EKPQDCGNSF EA [yezq at pro des]$ seqret test Reads and writes (returns) sequences Output sequence [z1bpc2.fasta]: [yezq at pro des]$ more z1bpc2.fasta >Z1BPC2 MELTSTRKKANAITSSILNR IAIRGQRKVA DALGINESQI SRWKGDFIPK MGMLLAVLEW GVEDEELAELAKKVAHLLTKEKPQDCGNSFEA ???? Is there anyone think that this is a bug? ???????????????? Best Regards! ????????????????????????????Zhiqiang Ye ??????????????????????????????????2004-07-20 ############################################################### Zhiqiang Ye, Ph. D candidate, Major in Bioinformatics Center of BioInformatics, College of Life Scicences, Peking University, Beijing, PR China 100871 Tel: +86 10 6275 6730 ############################################################### From pmr at ebi.ac.uk Tue Jul 20 06:20:26 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 20 Jul 2004 11:20:26 +0100 Subject: [EMBOSS] seqret problem? In-Reply-To: <200407201006.i6KA66i1014029@mail.cbi.pku.edu.cn> References: <200407201006.i6KA66i1014029@mail.cbi.pku.edu.cn> Message-ID: <40FCF1EA.1060106@ebi.ac.uk> Zhiqiang Ye wrote: > hi all?? > I find that if there is a semicolon in the description line, seqret works wrong. seqret works "correctly" ... but it is very confusing in this case. The ">P1;" format is PIR format for a complete protein (fragemnts have ">F1;"). The rest of the line is the ID. But in PIR format, the next line is the description - so EMBOSS will read the first line of your sequence as a description, which is why it appears on the first line of the FASTA format output. You will find "seqret -sf pir" works the same way, and "seqret -sf fasta" will complain about the sequence format. I think there is no way to avoid this problem - because EMBOSS does not know that the next line is not a sequence. Hope that make things clearer, Peter Rice >P1;Z1BPC2 MELTSTRKKANAITSSILNR IAIRGQRKVA DALGINESQI SRWKGDFIPK MGMLLAVLEW GVEDEELAEL AKKVAHLLTK EKPQDCGNSF EA [yezq at pro des]$ seqret test Reads and writes (returns) sequences Output sequence [z1bpc2.fasta]: [yezq at pro des]$ more z1bpc2.fasta >Z1BPC2 MELTSTRKKANAITSSILNR IAIRGQRKVA DALGINESQI SRWKGDFIPKMGMLLAVLEWGVEDEELAELAKKVAHLLTKEKPQDCGNSFEA From simon.andrews at bbsrc.ac.uk Tue Jul 20 06:42:43 2004 From: simon.andrews at bbsrc.ac.uk (simon andrews (BI)) Date: Tue, 20 Jul 2004 11:42:43 +0100 Subject: [EMBOSS] seqret problem? Message-ID: > -----Original Message----- > From: Zhiqiang Ye [mailto:yezq at mail.cbi.pku.edu.cn] > Sent: 20 July 2004 11:11 > To: emboss > Subject: [EMBOSS] seqret problem? > > > hi all > I find that if there is a semicolon in the description > line, seqret works wrong. > > [yezq at pro]$ more test > >P1;Z1BPC2 > MELTSTRKKANAITSSILNR IAIRGQRKVA DALGINESQI SRWKGDFIPK MGMLLAVLEW > GVEDEELAEL AKKVAHLLTK EKPQDCGNSF EA > > Is there anyone think that this is a bug? Yes, I'd say it's a bug, but possibly not in the form you presented it. In your example the problem is that seqret is incorrectly guessing the format of your sequence as NBRF. In this case your sequence is formatted in a way which could make it NBRF format so this is acceptable. What I think is a bug though is this: $ cat test.seq >P1;Z1BPC2 MELTSTRKKANAITSSILNR IAIRGQRKVA DALGINESQI SRWKGDFIPK MGMLLAVLEW GVEDEELAEL AKKVAHLLTK EKPQDCGNSF EA $ seqret fasta::test.seq fasta::stdout Reads and writes (returns) sequences Error: Unable to read sequence 'fasta::test.seq' Died: seqret terminated: Bad value for '-sequence' and no prompt Having looked at a few definitions of the fasta format I can't find one which says that your sequence doesn't conform to the standard. The semi-colon can be used in Fasta as a comment delimiter, so it could be argued that it would be correct to remove the Z1BPC completely in the output, but it should still parse OK. The problem seems to be that seqret is interpreting your sequence as the PIR subvariant of the FastA format (Strange, since the test FastA sequence I just got from PIR didn't have a semi-colon in the description line) and its subsequent tests on the file then fail. Since there doesn't seem to be a USA syntax for allowing you to specify which kind of FastA format you're using then I'd say this was a bug. If it guesses PIR and this subsequently fails then it should go back and use "dumb" FastA instead. Also, it's worth noting that whilst seqret can't read FastA files in this format it's more than happy to write them like that: $ cat test3.seq LOCUS P1;Z1BPC2 BASE COUNT 10 a 1 c 6 g 4 t 71 others ORIGIN 1 MELTSTRKKA NAITSSILNR IAIRGQRKVA DALGINESQI SRWKGDFIPK MGMLLAVLEW 61 GVEDEELAEL AKKVAHLLTK EKPQDCGNSF EA // $ seqret genbank::test3.seq fasta::test4.seq Reads and writes (returns) sequences $ seqret fasta::test4.seq fasta::stdout Reads and writes (returns) sequences Error: Unable to read sequence 'fasta::test4.seq' Died: seqret terminated: Bad value for '-sequence' and no prompt $ cat test4.seq >P1;Z1BPC2 MELTSTRKKANAITSSILNRIAIRGQRKVADALGINESQISRWKGDFIPKMGMLLAVLEW GVEDEELAELAKKVAHLLTKEKPQDCGNSFEA From pmr at ebi.ac.uk Tue Jul 20 07:18:22 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 20 Jul 2004 12:18:22 +0100 Subject: [EMBOSS] seqret problem? In-Reply-To: References: Message-ID: <40FCFF7E.30205@ebi.ac.uk> simon andrews (BI) wrote: > Having looked at a few definitions of the fasta format I can't find one > which says that your sequence doesn't conform to the standard. The > semi-colon can be used in Fasta as a comment delimiter, so it could be > argued that it would be correct to remove the Z1BPC completely in the > output, but it should still parse OK. > > The problem seems to be that seqret is interpreting your sequence as the > PIR subvariant of the FastA format (Strange, since the test FastA > sequence I just got from PIR didn't have a semi-colon in the description > line) and its subsequent tests on the file then fail. Fair enough. We do have to be careful about the automatic processing though. What we can do is to test the PIR/NBRF format ">P1:seqid" first (which we do), and then allow this as a valid FASTA format. I suspect earlier versions of EMBOSS would allow this format - but not since we tried to make sense of the NCBI's variants of FASTA format. At that point we realised there were various ways to read bad data by assuming a PIR first line is OK for FASTA format. I need to check through the details to see where this happens. We do have an alternative format "-sf pearson" which reads fasta files with less checking, and I can change this format to allow "PIR" fasta id lines through - but it is not tested by default because of the problems with auto-detecting the wrong format. > The problem seems to be that seqret is interpreting your sequence as the > PIR subvariant of the FastA format (Strange, since the test FastA > sequence I just got from PIR didn't have a semi-colon in the description > line) and its subsequent tests on the file then fail. > Sadly, PIR is not a subformat of FASTA ... it was the format used for the NBRF/PIR sequence analysis package. It has other odd features, not all of which are strictly used by EMBOSS (because most can be safely ignored :-) regards, Peter Rice From Fei.Zhong at qiagen.com Wed Jul 21 11:48:49 2004 From: Fei.Zhong at qiagen.com (Fei.Zhong at qiagen.com) Date: Wed, 21 Jul 2004 11:48:49 -0400 Subject: [EMBOSS] need help! Message-ID: Hello, I would like to use one tool, palindrome of EMBOSS. I downloaded the package EMBOSS-2.9.0.tar.gz and installed the whole package in my computer following the installation instruction. My computer OS is Sun Solaris Unix 9.0. I did not see any error message or special warning when I installed it. But while I try to run it, I got a problem. The error message is listed as follows: 54 fzhong at sirna:/export/home/fzhong/test/arrayProbe>/usr/local/bin/EMBOSS/b in/bin/palindrome ld.so.1: /usr/local/bin/EMBOSS/bin/bin/palindrome: fatal: libgcc_s.so.1: open failed: No such file or directory Killed Thanks so much in advance, Fei -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20040721/bc278292/attachment.html From Paul.Baumgartner at unibas.ch Thu Jul 22 11:27:19 2004 From: Paul.Baumgartner at unibas.ch (Paul Baumgartner) Date: Thu, 22 Jul 2004 17:27:19 +0200 Subject: [EMBOSS] weekday Message-ID: <9E902D94-DBF3-11D8-BD8F-003065B9531E@unibas.ch> Dear all fuzznuc seems to calculate the weekday wrong Output report [stdout]: ######################################## # Program: fuzznuc # Rundate: Sun Jul 22 16:08:24 2004 # Report_format: seqtable # Report_file: stdout ######################################## see rundate. Using 2.8.0 on macosx 10.3.4 thanks Paul Biozentrum Paul Baumgartner Zellbiologie Klingelbergstrasse 70 CH-4056 Basel From d.gatherer at vir.gla.ac.uk Fri Jul 23 05:52:11 2004 From: d.gatherer at vir.gla.ac.uk (Derek Gatherer) Date: Fri, 23 Jul 2004 10:52:11 +0100 Subject: [EMBOSS] incorporating old code in 2.9.0 Message-ID: <5.2.1.1.1.20040723083507.02dd7650@udcf.gla.ac.uk> Hi I have some local legacy code (written by a predecessor around 2000), which was successfully incorporated in 2.8.0. I used to get the CVS version of EMBOSS, stick the local *.c and *.acd in the relevant places, modify the Makefile.am, then run aclocal -I m4, autoconf -v, automake -a and then a configure, make and make install as usual. However, the old code is now failing at make with 2.9.0. The errors are slightly different for each but all are incompatible types in assignment. For instance, with one I get: incompatible type for argument 2 of `ajSeqReplace' and another: incompatible type for argument 1 of `ajStrChar' Is this because something has changed in nucleus/ajax etc which precludes the use of the old code? The only other thing that I think might be relevant is that I've recently upgraded my compiler to gcc-3.3.2, from a seriously old version. I'm still using autoconf-2.57 and automake-1.7.5. I can provide further details if this is not enough to diagnose. Cheers Derek _________________________ Derek Gatherer Ph.D. Cert.Ed. Computer Officer Institute of Virology Church St. Glasgow G11 5JR Phone: +44 141 330 6268 Fax: +44 141 337 2236 Email: d.gatherer at vir.gla.ac.uk Website: http://www.vir.gla.ac.uk From pmr at ebi.ac.uk Fri Jul 23 06:29:54 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 23 Jul 2004 11:29:54 +0100 Subject: [EMBOSS] incorporating old code in 2.9.0 In-Reply-To: <5.2.1.1.1.20040723083507.02dd7650@udcf.gla.ac.uk> References: <5.2.1.1.1.20040723083507.02dd7650@udcf.gla.ac.uk> Message-ID: <4100E8A2.70302@ebi.ac.uk> Derek Gatherer wrote: > However, the old code is now failing at make with 2.9.0. The errors are > slightly different for each but all are incompatible types in assignment. > > For instance, with one I get: > > incompatible type for argument 2 of `ajSeqReplace' > > and another: > > incompatible type for argument 1 of `ajStrChar' > > Is this because something has changed in nucleus/ajax etc which > precludes the use of the old code? Curious that you get errors. Passing an AjPStr to these functions should be fine. If you send me an example program it should be easy to fix. In cleaning up the code for 2.9.0 we have become strict about defining "const AjPStr" and "const char*" for read-only parameters. You may see some messages about return types - functions will now return a "const AjPStr" or a "const char*" which can cause you problems if you assign them to a non-const variable. Usually, copying them allows you to fix code easily. Tehre were some issues with the EMBOSS code, but nobody else using the current CVS code reported difficulties while we were nitroducing the changes. In the case of these two functions, the prototypes are now: void ajSeqReplace (AjPSeq thys, const AjPStr seq); char ajStrChar (const AjPStr thys, ajint pos); One issue is that the definition of AjPStr itself had to change to be a macro, so perhaps there is something strange with your include files or dependencies. AjPStr was part of the "typedef" for strings, but somehow compilers all fail to understand "const AjPStr" (they made the pointer constant) so it is now a macro that translates to "AjOStr*" and that means "const AjPStr" translates to "const AjOStr*" which is understood correctly by compilers (they make the string constant - strictly, they make the next level of the structure constant, which is all C compilers can do). By the way - we will all be in Glasgow next week for BOSC and ISMB - I expect we will see you there? regards, Peter Rice From kvddrift at earthlink.net Fri Jul 23 06:32:20 2004 From: kvddrift at earthlink.net (Koen van der Drift) Date: Fri, 23 Jul 2004 06:32:20 -0400 Subject: [EMBOSS] emboss, rebase and fink Message-ID: <93B17242-DC93-11D8-8F60-003065A5FDCC@earthlink.net> Hi, From an fink/emboss user I got a request to make a fink-package for rebase that will install the files proto and withrefm using rebaseextract. I got this all to work, but rebaseextract installs the files directly into the main fink tree, instead of in the fink required location where packages are built. So I need to patch the code for the package to be submitted to fink. I checked rebaseextract.c (and ajFile.c) and found that the location where rebaseextract puts the file is more or less hard-coded into the emboss code. Is there a way I can manipulate this location for the fink package, eg by replacing the calls to ajFileDataNewWrite() with one that accepts a user defined location? thanks, - Koen. From pmr at ebi.ac.uk Fri Jul 23 07:14:57 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 23 Jul 2004 12:14:57 +0100 Subject: [EMBOSS] incorporating old code in 2.9.0 In-Reply-To: <5.2.1.1.1.20040723115152.02dd6770@udcf.gla.ac.uk> References: <5.2.1.1.1.20040723083507.02dd7650@udcf.gla.ac.uk> <5.2.1.1.1.20040723083507.02dd7650@udcf.gla.ac.uk> <5.2.1.1.1.20040723115152.02dd6770@udcf.gla.ac.uk> Message-ID: <4100F331.5080002@ebi.ac.uk> Derek Gatherer wrote: (see Derek's previous message to emboss at embnet.org for the problem - copied to emboss-dev because developers will need to know the answer). Solution: All variable declarations of the type: AjPStr astr, bstr; must be split into single variables from EMBOSS 2.9.0: AjPStr astr; AjPStr bstr; Explanation follows. > Hi Peter > > Here is the full error set for one of the apps: > > compact.c: In function `main': > compact.c:53: error: incompatible types in assignment > > and the code is attached. > > #include "emboss.h" > int main (int argc, char **argv) > { > AjPStr cseq, cseqo; > cseq = ajStrNew(); > cseqo = ajStrNew(); Ah, all is now clear. I just kept the relevant lines included above. Note that the cseq line is fine, the cseqo line is the one that gives the error. The cause is the redefinition of AjPStr as a macro to make "const AjPStr" work. Sorry, I forgot to stress this one in the release notes. The problem is the line: AjPStr cseq, cseqo; Because AjPStr is now a macro that is replaced by "const AjOStr*" the definition of cseqo becomes: const AjOStr* cseq, cseqo; This is a classic C problem - cseq is now an AjPStr, cseqo is only an AjOStr (what an AjPStr points to). The solution ... AjPStr cseq; AjPStr cseqo; All AjP definitions have to now be one per line. Sorry - we worked very hard to avouid this, but the compilers simply fail to put the const in the right place otherwise so we have to live with the macro and this side effect. This should solve your problems. regards, Peter Rice From jrvalverde at cnb.uam.es Fri Jul 23 08:27:51 2004 From: jrvalverde at cnb.uam.es (=?ISO-8859-15?Q?Jos=E9?= R. Valverde) Date: Fri, 23 Jul 2004 14:27:51 +0200 Subject: [EMBOSS] incorporating old code in 2.9.0 In-Reply-To: <4100F331.5080002@ebi.ac.uk> References: <5.2.1.1.1.20040723083507.02dd7650@udcf.gla.ac.uk> <5.2.1.1.1.20040723083507.02dd7650@udcf.gla.ac.uk> <5.2.1.1.1.20040723115152.02dd6770@udcf.gla.ac.uk> <4100F331.5080002@ebi.ac.uk> Message-ID: <20040723142751.628764c8.jrvalverde@cnb.uam.es> > Because AjPStr is now a macro that is replaced by "const AjOStr*" the > definition of cseqo becomes: > > const AjOStr* cseq, cseqo; > > This is a classic C problem - cseq is now an AjPStr, cseqo is only an AjOStr > (what an AjPStr points to). > Excuse me, but I've got a doubt regarding this. Wouldn't typedef const AjOStr * AjPStr; fix this and allow for multiple declarations in the same line? j -- These opinions are mine and only mine. Hey man, I saw them first! Jos? R. Valverde De nada sirve la Inteligencia Artificial cuando falta la Natural From justbeforeme at hotmail.com Sun Jul 25 23:51:38 2004 From: justbeforeme at hotmail.com (kenix y) Date: Mon, 26 Jul 2004 11:51:38 +0800 Subject: [EMBOSS] error in ajacd.c Message-ID: Hi, When I try to run any emboss application, I got the following error: error while loading shared libraries: libnucleus.so.0: cannot open shared object file: no such file or directory. But the file is located at /opt/BioBrew/EMBOSS/2.6.0/lib/ After I tried to set up the environment for using EMBOSS in ~/.bashrc export LD_LIBRARY_PATH=/opt/BioBrew/EMBOSS/2.6.0/lib:$LD_LIBRARY_PATH the error changed to EMBOSS An error in ajacd.c at line 1534: acdfile '/home/build/BuildRoot-ia32/BUILD/EMBOSS-2.6.0/emboss/acd/wossname.acd' not opened. Does anyone knows how to solve this? Thank you Rgds, kenix _________________________________________________________________ Get 10mb of inbox space with MSN Hotmail Extra Storage http://join.msn.com/?pgmarket=en-sg From Bent.Terp at biosci.ki.se Mon Jul 26 02:26:52 2004 From: Bent.Terp at biosci.ki.se (Bent Terp) Date: Mon, 26 Jul 2004 08:26:52 +0200 Subject: [EMBOSS] error in ajacd.c In-Reply-To: References: Message-ID: <1090823212.8703.2.camel@latte> On Mon, 2004-07-26 at 05:51, kenix y wrote: > Hi, > > When I try to run any emboss application, I got the following error: > error while loading shared libraries: libnucleus.so.0: cannot open shared > object file: no such file or directory. > But the file is located at /opt/BioBrew/EMBOSS/2.6.0/lib/ > > After I tried to set up the environment for using EMBOSS in ~/.bashrc > export LD_LIBRARY_PATH=/opt/BioBrew/EMBOSS/2.6.0/lib:$LD_LIBRARY_PATH > > the error changed to > EMBOSS An error in ajacd.c at line 1534: acdfile > '/home/build/BuildRoot-ia32/BUILD/EMBOSS-2.6.0/emboss/acd/wossname.acd' not > opened. > > Does anyone knows how to solve this? You need your environment set up as in the installation docs. Basically add this to your .bashrc: declare -x EMBOSS_ACDROOT="/usr/share/EMBOSS/acd" declare -x EMBOSS_DATA="/usr/share/EMBOSS/data" declare -x EMBOSS_DATABASE_DIR="/usr/share/EMBOSS/data" declare -x EMBOSS_DOCROOT="/usr/share/EMBOSS/doc" substituting /opt/BioBrew/EMBOSS for /usr/share/EMBOSS alternatively, if you're using redhat, you can install EMBOSS through declare -x EMBOSS_DATA="/usr/share/EMBOSS/data" >declare -x EMBOSS_DATABASE_DIR="/usr/share/EMBOSS/data" >declare -x EMBOSS_DOCROOT="/usr/share/EMBOSS/doc" I find them in /opt/BioBrew/EMBOSS/2.6.0/share/EMBOSS Should the paths be changed to >declare -x EMBOSS_ACDROOT="/opt/BioBrew/EMBOSS/2.6.0/share/EMBOSS/acd" >declare -x EMBOSS_DATA="/opt/BioBrew/EMBOSS/2.6.0/share/EMBOSS/data" >declare -x >EMBOSS_DATABASE_DIR="/opt/BioBrew/EMBOSS/2.6.0/share/EMBOSS/data" >declare -x EMBOSS_DOCROOT="/opt/BioBrew/EMBOSS/2.6.0/share/EMBOSS/doc" in my case? Thank you. >From: Bent Terp >To: EMBOSS list >Subject: Re: [EMBOSS] error in ajacd.c >Date: Mon, 26 Jul 2004 08:26:52 +0200 > >On Mon, 2004-07-26 at 05:51, kenix y wrote: > > Hi, > > > > When I try to run any emboss application, I got the following error: > > error while loading shared libraries: libnucleus.so.0: cannot open >shared > > object file: no such file or directory. > > But the file is located at /opt/BioBrew/EMBOSS/2.6.0/lib/ > > > > After I tried to set up the environment for using EMBOSS in ~/.bashrc > > export LD_LIBRARY_PATH=/opt/BioBrew/EMBOSS/2.6.0/lib:$LD_LIBRARY_PATH > > > > the error changed to > > EMBOSS An error in ajacd.c at line 1534: acdfile > > '/home/build/BuildRoot-ia32/BUILD/EMBOSS-2.6.0/emboss/acd/wossname.acd' >not > > opened. > > > > Does anyone knows how to solve this? > >You need your environment set up as in the installation docs. Basically >add this to your .bashrc: >declare -x EMBOSS_ACDROOT="/usr/share/EMBOSS/acd" >declare -x EMBOSS_DATA="/usr/share/EMBOSS/data" >declare -x EMBOSS_DATABASE_DIR="/usr/share/EMBOSS/data" >declare -x EMBOSS_DOCROOT="/usr/share/EMBOSS/doc" > >substituting /opt/BioBrew/EMBOSS for /usr/share/EMBOSS > > alternatively, if you're using redhat, you can >install EMBOSS through >declare -x EMBOSS_DATA="/usr/share/EMBOSS/data" > >declare -x EMBOSS_DATABASE_DIR="/usr/share/EMBOSS/data" > >declare -x EMBOSS_DOCROOT="/usr/share/EMBOSS/doc" > > I find them in /opt/BioBrew/EMBOSS/2.6.0/share/EMBOSS > > Should the paths be changed to > >declare -x EMBOSS_ACDROOT="/opt/BioBrew/EMBOSS/2.6.0/share/EMBOSS/acd" > >declare -x EMBOSS_DATA="/opt/BioBrew/EMBOSS/2.6.0/share/EMBOSS/data" > >declare -x > >EMBOSS_DATABASE_DIR="/opt/BioBrew/EMBOSS/2.6.0/share/EMBOSS/data" > >declare -x EMBOSS_DOCROOT="/opt/BioBrew/EMBOSS/2.6.0/share/EMBOSS/doc" > > in my case? If you have a dir called /opt/BioBrew/EMBOSS/2.6.0/share/EMBOSS/acd then yes Out of sheer curiosity, what else have you got installed in /opt/BioBrew? Merely interested to know of other apps I should add to BioRPMS.... > > Thank you. > > >From: Bent Terp > >To: EMBOSS list > >Subject: Re: [EMBOSS] error in ajacd.c > >Date: Mon, 26 Jul 2004 08:26:52 +0200 > > > >On Mon, 2004-07-26 at 05:51, kenix y wrote: > > > Hi, > > > > > > When I try to run any emboss application, I got the following error: > > > error while loading shared libraries: libnucleus.so.0: cannot open > >shared > > > object file: no such file or directory. > > > But the file is located at /opt/BioBrew/EMBOSS/2.6.0/lib/ > > > > > > After I tried to set up the environment for using EMBOSS in ~/.bashrc > > > export LD_LIBRARY_PATH=/opt/BioBrew/EMBOSS/2.6.0/lib:$LD_LIBRARY_PATH > > > > > > the error changed to > > > EMBOSS An error in ajacd.c at line 1534: acdfile > > > '/home/build/BuildRoot-ia32/BUILD/EMBOSS-2.6.0/emboss/acd/wossname.acd' > >not > > > opened. > > > > > > Does anyone knows how to solve this? > > > >You need your environment set up as in the installation docs. Basically > >add this to your .bashrc: > >declare -x EMBOSS_ACDROOT="/usr/share/EMBOSS/acd" > >declare -x EMBOSS_DATA="/usr/share/EMBOSS/data" > >declare -x EMBOSS_DATABASE_DIR="/usr/share/EMBOSS/data" > >declare -x EMBOSS_DOCROOT="/usr/share/EMBOSS/doc" > > > >substituting /opt/BioBrew/EMBOSS for /usr/share/EMBOSS > > > > alternatively, if you're using redhat, you can > >install EMBOSS through References: <4100E8A2.70302@ebi.ac.uk> <5.2.1.1.1.20040723083507.02dd7650@udcf.gla.ac.uk> <5.2.1.1.1.20040723083507.02dd7650@udcf.gla.ac.uk> Message-ID: <5.2.1.1.1.20040726102546.02dff1c0@udcf.gla.ac.uk> and the same applies to AjPFloat, ie: AjPFloat matrixa; AjPFloat matrixb; AjPFloat matrixc; AjPFloat matrixe; is necessary. At 09:56 26/07/2004 +0100, Derek Gatherer wrote: >At 11:29 23/07/2004 +0100, Peter Rice wrote: > >>In cleaning up the code for 2.9.0 we have become strict about defining >>"const AjPStr" and "const char*" for read-only parameters. > >It seems that AjPFile variable also need to be declared one line at a time >too. Eg: > >This compiles okay: > >int main (int argc, char **argv) >{ > AjPFile fhmatina; // all AjPFile need own lines for 2.9.0 > AjPFile fhmatinb; > AjPFile fhoutmat; > AjPStr linea; // all AjPStr need own lines for 2.9.0 > AjPStr lineb; > AjPStr elementa; > AjPStr elementb; > ajint i, j, seqsina, seqsinb; > float ftmpa, ftmpb, sigmax2=0, sigmax=0, xsigmax2=0, xsigmax=0; > float mean, xmean, sdsample, sdpopulation, xsdsample, xsdpopulation; > float gbrate; > char *ctmp; > >but this crashes at make with the same "incompatible types in assignment" >error. > >int main (int argc, char **argv) >{ > AjPFile fhmatina, fhmatinb, fhoutmat; > AjPStr linea; // all AjPStr need own lines for 2.9.0 > AjPStr lineb; > AjPStr elementa; > AjPStr elementb; > ajint i, j, seqsina, seqsinb; > float ftmpa, ftmpb, sigmax2=0, sigmax=0, xsigmax2=0, xsigmax=0; > float mean, xmean, sdsample, sdpopulation, xsdsample, xsdpopulation; > float gbrate; > char *ctmp; > >I'm still making, so if I find anything else, I'll let you know. I'm >about halfway through make, and so far this is the only additional error. > >cheers >Derek >_________________________ > >Derek Gatherer Ph.D. Cert.Ed. >Computer Officer >Institute of Virology >Church St. >Glasgow G11 5JR > >Phone: +44 141 330 6268 >Fax: +44 141 337 2236 >Email: d.gatherer at vir.gla.ac.uk >Website: http://www.vir.gla.ac.uk _________________________ Derek Gatherer Ph.D. Cert.Ed. Computer Officer Institute of Virology Church St. Glasgow G11 5JR Phone: +44 141 330 6268 Fax: +44 141 337 2236 Email: d.gatherer at vir.gla.ac.uk Website: http://www.vir.gla.ac.uk From bobby_rgm at yahoo.com Wed Jul 28 07:34:08 2004 From: bobby_rgm at yahoo.com (chowdary manio) Date: Wed, 28 Jul 2004 04:34:08 -0700 (PDT) Subject: [EMBOSS] protein sequence input Message-ID: <20040728113408.58345.qmail@web53207.mail.yahoo.com> hi, I am using the emboss to make protein sequence analysis. I want the program "water"(smith-waterman algorithm) to take in the characters "J","O","U" which are not aminoacid symbols. Can I change the code?, If so, in which file I have to make this change, to make the program take this desired input Thank you, bobby __________________________________ Do you Yahoo!? New and Improved Yahoo! Mail - 100MB free storage! http://promotions.yahoo.com/new_mail From pmr at ebi.ac.uk Wed Jul 28 10:13:37 2004 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Wed, 28 Jul 2004 15:13:37 +0100 (BST) Subject: [EMBOSS] protein sequence input In-Reply-To: <20040728113408.58345.qmail@web53207.mail.yahoo.com> References: <20040728113408.58345.qmail@web53207.mail.yahoo.com> Message-ID: <40552.217.45.210.49.1091024017.squirrel@webmail.ebi.ac.uk> Hi Bobby, > I am using the emboss to make protein sequence > analysis. > > I want the program "water"(smith-waterman algorithm) > to take in the characters "J","O","U" which are not > aminoacid symbols. > > Can I change the code?, If so, in which file I have to > make this change, to make the program take this > desired input Interesting question. The sequence types are checked in ajax/ajseqtype.c But there is also the question of whether your sequence is really a protein. Perhaps we should allow "alpha" as a sequence type, with its own comparison matrices. It could get complicated (we need to check whether we assume all non-nucleic sequences are protein, for example). "U" is a valid protein code (for selenocysteine). "O" is used as a gap character by some formats. "J" is not used. I have seen "O" and "J" used in modified matrices before - though that was as DNA to score CpG islands differently (CG was converted to OJ and given higher match scores) Perhaps, as a quick solution, you could try using the protein ambiguity codes B and Z instead of O and J? Then you could use a normal protein sequence. Hope that helps, Peter From ableasby at hgmp.mrc.ac.uk Thu Jul 15 17:58:49 2004 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Thu, 15 Jul 2004 18:58:49 +0100 (BST) Subject: [EMBOSS] EMBOSS 2.9.0 released Message-ID: <200407151758.i6FHwnkW007992@bromine.hgmp.mrc.ac.uk> This email announces the release of EMBOSS 2.9.0; the traditional St Swithin's Day release prior to the ISMB conference. Many of the EMBOSS developers will be at ISMB. There will be an EMBOSS talk at BOSC, three related ISMB demonstrations (EMBOSS, JEMBOSS and Taverna) and we'll be present at the poster session. We hope to see you there. EMBOSS 2.9.0 can be downloaded via the new web site (emboss.sf.net) which we encourage people to start using. At present the download will be directed to the RFCGR ftp server; this will be changed. The old web site (www.rfcgr.mrc.ac.uk/Software/EMBOSS) will be removed within the year. Please note that the emboss.org domain has never been owned by the EMBOSS core developers so we have no control over any popups appearing on that site. As usual the changes appear in the ChangeLog file. A major feature of this release is extensive modifications to ACD and the libraries as part of the development of an EMBOSS ontology. This is to allow future provision of workflow analysis. The EMBASSY packages can now be compiled and linked against an installed version of EMBOSS. There is no need to retain the EMBOSS sources. This can be done from any directory. You just need to provide an appropriate --prefix= option to the configure command. The only exception is if you have installed EMBOSS in /usr/local/bin and associated directories. In this one case you must give the --enable-localforce option to your EMBASSY configure command as well. This does not apply to, for example, installations into /usr/local/emboss or any other directory hierarchy under /usr/local (the --prefix= option is enough). Older downloads of the EMBASSY packages will not work with 2.9.0; you should download them again. The decision of the MRC to close the RFCGR (see appended URL) has delayed the completion of several improvements (e.g. indexing, the new graphics library and the ACD ontology). We hope to get these out in the next release. We are, however, still seeking alternative sources of funding so it would therefore be unwise for us to give any firm assurances. Alan For the official MRC announcement of the closure of the RFCGR see: http://www.mrc.ac.uk/index/public-interest/public-council_meetings/ public-council_meetings_2003-04/public-council_meetings_31_mar04/ public-council_meeting_31_mar04_note.htm From hegedus at biomembrane.hu Thu Jul 15 18:31:11 2004 From: hegedus at biomembrane.hu (Tamas Hegedus) Date: Thu, 15 Jul 2004 20:31:11 +0200 (CEST) Subject: [EMBOSS] ModBioSQL release 0.12 Message-ID: Dear All, during my work I had to use RDBMS and EMBOSS. I collected my scripts and experiments into a package called Modular BioSQL, which has different features: -- Modular RDB realization of different biological databases allows fine-tuning with increased performance. -- Storing result sets in RDBMS allows more accurate, more comfortable analysis using SQL. -- User interaction with the RDBMS (installation, loading up and querying data) does not need programming skills. -- Light weight RDB interaction with analysis packages (only EMBOSS is implemented). -- Optimalized loading of flat files into the RDBMS. -- Using 'fixed value arrays' (*_ref tables) results in both smaller data size (smaller than the flat file) and smaller index size increasing the performance (theoretically both the uploading and querying performance). -- Relatively easily extendable to implement and handle databases other than the currently realized. You may think I suggest Modular BioSQL as a replacement of BioSQL. I do not think so! For details, please visit my web site, and send comments and suggestions: http://www.biomembrane.hu/~hegedus/modbiosql/ Best regards, Tamas -- Tam?s Heged?s, Research Associate | http://www.biomembrane.hu Membrane Research Group of | mailto:hegedus at biomembrane.hu Hungarian Academy of Sciences | tel: 36-1-3724317 H-1113 Budapest Dioszegi u 64, HUNGARY | fax: 36-1-3724353 From rsucgang at bcm.tmc.edu Thu Jul 15 22:32:40 2004 From: rsucgang at bcm.tmc.edu (richard sucgang phd) Date: Thu, 15 Jul 2004 17:32:40 -0500 Subject: [EMBOSS] sirna module In-Reply-To: <200407151758.i6FHwnkW007992@bromine.hgmp.mrc.ac.uk> References: <200407151758.i6FHwnkW007992@bromine.hgmp.mrc.ac.uk> Message-ID: Congratulations on the release of EMBOSS 2.9 I have been trying to use the sirna design program in EMBOSS, but have been getting a cryptic bus error message as it dies. I thought this may have been fixed in the newest version, but after compiling and installing, I get the same error. I am using MacOS X 10.3.4, with gobs of RAM, and a straightforward FASTA file. Any ideas as to what's going on? Thanks. -- Richard Sucgang, PhD (713) 798 7657 http://www.dictygenome.org/ From David.Bauer at SCHERING.DE Fri Jul 16 06:58:46 2004 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Fri, 16 Jul 2004 08:58:46 +0200 Subject: Antwort: [EMBOSS] sirna module Message-ID: This seems to be specific to MacOS X. I just updated to 2.9 on FreeBSD 4.9 and sirna is OK. (I also had no problems with sirna in 2.8, on Solaris and FreeBSD). David. richard sucgang phd Kopie: Gesendet von: Thema: [EMBOSS] sirna module owner-emboss at hgm p.mrc.ac.uk 16.07.2004 00:32 Congratulations on the release of EMBOSS 2.9 I have been trying to use the sirna design program in EMBOSS, but have been getting a cryptic bus error message as it dies. I thought this may have been fixed in the newest version, but after compiling and installing, I get the same error. I am using MacOS X 10.3.4, with gobs of RAM, and a straightforward FASTA file. Any ideas as to what's going on? Thanks. -- Richard Sucgang, PhD (713) 798 7657 http://www.dictygenome.org/ From d.gatherer at vir.gla.ac.uk Fri Jul 16 12:29:05 2004 From: d.gatherer at vir.gla.ac.uk (Derek Gatherer) Date: Fri, 16 Jul 2004 13:29:05 +0100 Subject: [EMBOSS] EMBOSS 2.9.0 released In-Reply-To: <200407151758.i6FHwnkW007992@bromine.hgmp.mrc.ac.uk> Message-ID: <5.2.1.1.1.20040716132757.00b160d0@udcf.gla.ac.uk> Hi Will cvs still be usable? cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/emboss login or does that have to be pointed at emboss.sf.net too? thanks Derek At 18:58 15/07/2004 +0100, Alan Bleasby wrote: >This email announces the release of EMBOSS 2.9.0; the traditional St >Swithin's Day release prior to the ISMB conference. Many of the EMBOSS >developers will be at ISMB. There will be an EMBOSS talk at BOSC, >three related ISMB demonstrations (EMBOSS, JEMBOSS and Taverna) and >we'll be present at the poster session. We hope to see you there. > >EMBOSS 2.9.0 can be downloaded via the new web site (emboss.sf.net) >which we encourage people to start using. At present the download will >be directed to the RFCGR ftp server; this will be changed. The old web >site (www.rfcgr.mrc.ac.uk/Software/EMBOSS) will be removed within the >year. Please note that the emboss.org domain has never been owned by >the EMBOSS core developers so we have no control over any popups >appearing on that site. > >As usual the changes appear in the ChangeLog file. A >major feature of this release is extensive modifications to ACD and >the libraries as part of the development of an EMBOSS ontology. This >is to allow future provision of workflow analysis. > >The EMBASSY packages can now be compiled and linked against an >installed version of EMBOSS. There is no need to retain the EMBOSS >sources. This can be done from any directory. You just need to provide >an appropriate --prefix= option to the configure command. The only >exception is if you have installed EMBOSS in /usr/local/bin and >associated directories. In this one case you must give the >--enable-localforce option to your EMBASSY configure command as >well. This does not apply to, for example, installations into >/usr/local/emboss or any other directory hierarchy under /usr/local >(the --prefix= option is enough). Older downloads of the EMBASSY >packages will not work with 2.9.0; you should download them again. > >The decision of the MRC to close the RFCGR (see appended URL) has >delayed the completion of several improvements (e.g. indexing, the new >graphics library and the ACD ontology). We hope to get these out in >the next release. We are, however, still seeking alternative sources >of funding so it would therefore be unwise for us to give any firm >assurances. > >Alan > >For the official MRC announcement of the closure of the RFCGR see: >http://www.mrc.ac.uk/index/public-interest/public-council_meetings/ >public-council_meetings_2003-04/public-council_meetings_31_mar04/ >public-council_meeting_31_mar04_note.htm _________________________ Derek Gatherer Ph.D. Cert.Ed. Computer Officer Institute of Virology Church St. Glasgow G11 5JR Phone: +44 141 330 6268 Fax: +44 141 337 2236 Email: d.gatherer at vir.gla.ac.uk Website: http://www.vir.gla.ac.uk From ableasby at hgmp.mrc.ac.uk Fri Jul 16 12:43:54 2004 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Fri, 16 Jul 2004 13:43:54 +0100 (BST) Subject: [EMBOSS] EMBOSS 2.9.0 released Message-ID: <200407161243.i6GChsKN022768@bromine.hgmp.mrc.ac.uk> Hello Derek, CVS will indeed still be usable from open-bio.org. There is no immediate intention to put a cvs server on sourceforge. Alan From pmr at ebi.ac.uk Fri Jul 16 12:43:56 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 16 Jul 2004 13:43:56 +0100 Subject: [EMBOSS] EMBOSS 2.9.0 released In-Reply-To: <5.2.1.1.1.20040716132757.00b160d0@udcf.gla.ac.uk> References: <5.2.1.1.1.20040716132757.00b160d0@udcf.gla.ac.uk> Message-ID: <40F7CD8C.6060107@ebi.ac.uk> Derek Gatherer wrote: > Will cvs still be usable? > > cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/emboss login > > or does that have to be pointed at emboss.sf.net too? We will be keeping the present CVS. Open Bio has been a good host, so we see no need to relocate CVS to Sourceforge. We relocated once before (in July 2000, from Sanger to open-bio) and would prefer not to move again. We will have to relocate a few things that are still at RFCGR: * The FTP server (that's where ftp.uk.embnet.org is) * The mailing list archives * The EFUNC and EDATA SRS databases (they can move to EBI) We aim to mirror everything ASAP in their new homes. The emboss.sourceforge.net website already has most of the content of the RFCGR (www.emboss.org) website. regards, Peter Rice From Bent.Terp at biosci.ki.se Fri Jul 16 13:08:16 2004 From: Bent.Terp at biosci.ki.se (Bent Terp) Date: Fri, 16 Jul 2004 15:08:16 +0200 Subject: [EMBOSS] Jemboss in local mode Message-ID: <1089983296.10815.64.camel@latte.biosci.ki.se> Hi all! I've been working a bit on producing RPM's of EMBOSS and friends, but still have a problem: When I launch jemboss in local mode, no window gets created but lots of cpu-time consumed. Are there any debug options that will reveal more? I've attached the launch script and jemboss.properties in case that helps. -- MVH / With kind regards, Bent Terp System Administrator Bioinformatics and Expression Analysis Core Facility Karolinska Institute, Department of Biosciences H?lsovagen 7-9, 141 57 Huddinge, Sweden -------------- next part -------------- A non-text attachment was scrubbed... Name: jemboss Type: text/x-sh Size: 1788 bytes Desc: not available URL: -------------- next part -------------- user.auth=false jemboss.server=false plplot=/usr/share/EMBOSS/ embossData=/usr/share/EMBOSS/data/ embossBin=/usr/bin/ embossPath=/usr/bin:/bin:/packages/clustal/:/packages/primer3/bin:/data/jobqueue/bin/:/usr/ucb/ acdDirToParse=/usr/share/EMBOSS/acd/ embossURL=http://www.uk.embnet.org/Software/EMBOSS/Apps/ From yezq at mail.cbi.pku.edu.cn Tue Jul 20 10:10:43 2004 From: yezq at mail.cbi.pku.edu.cn (Zhiqiang Ye) Date: Tue, 20 Jul 2004 18:10:43 +0800 Subject: [EMBOSS] seqret problem? Message-ID: <200407201006.i6KA66i1014029@mail.cbi.pku.edu.cn> hi all? I find that if there is a semicolon in the description line, seqret works wrong. [yezq at pro]$ more test >P1;Z1BPC2 MELTSTRKKANAITSSILNR IAIRGQRKVA DALGINESQI SRWKGDFIPK MGMLLAVLEW GVEDEELAEL AKKVAHLLTK EKPQDCGNSF EA [yezq at pro des]$ seqret test Reads and writes (returns) sequences Output sequence [z1bpc2.fasta]: [yezq at pro des]$ more z1bpc2.fasta >Z1BPC2 MELTSTRKKANAITSSILNR IAIRGQRKVA DALGINESQI SRWKGDFIPK MGMLLAVLEW GVEDEELAELAKKVAHLLTKEKPQDCGNSFEA ?? Is there anyone think that this is a bug? ???????? Best Regards! ??????????????Zhiqiang Ye ?????????????????2004-07-20 ############################################################### Zhiqiang Ye, Ph. D candidate, Major in Bioinformatics Center of BioInformatics, College of Life Scicences, Peking University, Beijing, PR China 100871 Tel: +86 10 6275 6730 ############################################################### From pmr at ebi.ac.uk Tue Jul 20 10:20:26 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 20 Jul 2004 11:20:26 +0100 Subject: [EMBOSS] seqret problem? In-Reply-To: <200407201006.i6KA66i1014029@mail.cbi.pku.edu.cn> References: <200407201006.i6KA66i1014029@mail.cbi.pku.edu.cn> Message-ID: <40FCF1EA.1060106@ebi.ac.uk> Zhiqiang Ye wrote: > hi all? > I find that if there is a semicolon in the description line, seqret works wrong. seqret works "correctly" ... but it is very confusing in this case. The ">P1;" format is PIR format for a complete protein (fragemnts have ">F1;"). The rest of the line is the ID. But in PIR format, the next line is the description - so EMBOSS will read the first line of your sequence as a description, which is why it appears on the first line of the FASTA format output. You will find "seqret -sf pir" works the same way, and "seqret -sf fasta" will complain about the sequence format. I think there is no way to avoid this problem - because EMBOSS does not know that the next line is not a sequence. Hope that make things clearer, Peter Rice >P1;Z1BPC2 MELTSTRKKANAITSSILNR IAIRGQRKVA DALGINESQI SRWKGDFIPK MGMLLAVLEW GVEDEELAEL AKKVAHLLTK EKPQDCGNSF EA [yezq at pro des]$ seqret test Reads and writes (returns) sequences Output sequence [z1bpc2.fasta]: [yezq at pro des]$ more z1bpc2.fasta >Z1BPC2 MELTSTRKKANAITSSILNR IAIRGQRKVA DALGINESQI SRWKGDFIPKMGMLLAVLEWGVEDEELAELAKKVAHLLTKEKPQDCGNSFEA From simon.andrews at bbsrc.ac.uk Tue Jul 20 10:42:43 2004 From: simon.andrews at bbsrc.ac.uk (simon andrews (BI)) Date: Tue, 20 Jul 2004 11:42:43 +0100 Subject: [EMBOSS] seqret problem? Message-ID: > -----Original Message----- > From: Zhiqiang Ye [mailto:yezq at mail.cbi.pku.edu.cn] > Sent: 20 July 2004 11:11 > To: emboss > Subject: [EMBOSS] seqret problem? > > > hi all > I find that if there is a semicolon in the description > line, seqret works wrong. > > [yezq at pro]$ more test > >P1;Z1BPC2 > MELTSTRKKANAITSSILNR IAIRGQRKVA DALGINESQI SRWKGDFIPK MGMLLAVLEW > GVEDEELAEL AKKVAHLLTK EKPQDCGNSF EA > > Is there anyone think that this is a bug? Yes, I'd say it's a bug, but possibly not in the form you presented it. In your example the problem is that seqret is incorrectly guessing the format of your sequence as NBRF. In this case your sequence is formatted in a way which could make it NBRF format so this is acceptable. What I think is a bug though is this: $ cat test.seq >P1;Z1BPC2 MELTSTRKKANAITSSILNR IAIRGQRKVA DALGINESQI SRWKGDFIPK MGMLLAVLEW GVEDEELAEL AKKVAHLLTK EKPQDCGNSF EA $ seqret fasta::test.seq fasta::stdout Reads and writes (returns) sequences Error: Unable to read sequence 'fasta::test.seq' Died: seqret terminated: Bad value for '-sequence' and no prompt Having looked at a few definitions of the fasta format I can't find one which says that your sequence doesn't conform to the standard. The semi-colon can be used in Fasta as a comment delimiter, so it could be argued that it would be correct to remove the Z1BPC completely in the output, but it should still parse OK. The problem seems to be that seqret is interpreting your sequence as the PIR subvariant of the FastA format (Strange, since the test FastA sequence I just got from PIR didn't have a semi-colon in the description line) and its subsequent tests on the file then fail. Since there doesn't seem to be a USA syntax for allowing you to specify which kind of FastA format you're using then I'd say this was a bug. If it guesses PIR and this subsequently fails then it should go back and use "dumb" FastA instead. Also, it's worth noting that whilst seqret can't read FastA files in this format it's more than happy to write them like that: $ cat test3.seq LOCUS P1;Z1BPC2 BASE COUNT 10 a 1 c 6 g 4 t 71 others ORIGIN 1 MELTSTRKKA NAITSSILNR IAIRGQRKVA DALGINESQI SRWKGDFIPK MGMLLAVLEW 61 GVEDEELAEL AKKVAHLLTK EKPQDCGNSF EA // $ seqret genbank::test3.seq fasta::test4.seq Reads and writes (returns) sequences $ seqret fasta::test4.seq fasta::stdout Reads and writes (returns) sequences Error: Unable to read sequence 'fasta::test4.seq' Died: seqret terminated: Bad value for '-sequence' and no prompt $ cat test4.seq >P1;Z1BPC2 MELTSTRKKANAITSSILNRIAIRGQRKVADALGINESQISRWKGDFIPKMGMLLAVLEW GVEDEELAELAKKVAHLLTKEKPQDCGNSFEA From pmr at ebi.ac.uk Tue Jul 20 11:18:22 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 20 Jul 2004 12:18:22 +0100 Subject: [EMBOSS] seqret problem? In-Reply-To: References: Message-ID: <40FCFF7E.30205@ebi.ac.uk> simon andrews (BI) wrote: > Having looked at a few definitions of the fasta format I can't find one > which says that your sequence doesn't conform to the standard. The > semi-colon can be used in Fasta as a comment delimiter, so it could be > argued that it would be correct to remove the Z1BPC completely in the > output, but it should still parse OK. > > The problem seems to be that seqret is interpreting your sequence as the > PIR subvariant of the FastA format (Strange, since the test FastA > sequence I just got from PIR didn't have a semi-colon in the description > line) and its subsequent tests on the file then fail. Fair enough. We do have to be careful about the automatic processing though. What we can do is to test the PIR/NBRF format ">P1:seqid" first (which we do), and then allow this as a valid FASTA format. I suspect earlier versions of EMBOSS would allow this format - but not since we tried to make sense of the NCBI's variants of FASTA format. At that point we realised there were various ways to read bad data by assuming a PIR first line is OK for FASTA format. I need to check through the details to see where this happens. We do have an alternative format "-sf pearson" which reads fasta files with less checking, and I can change this format to allow "PIR" fasta id lines through - but it is not tested by default because of the problems with auto-detecting the wrong format. > The problem seems to be that seqret is interpreting your sequence as the > PIR subvariant of the FastA format (Strange, since the test FastA > sequence I just got from PIR didn't have a semi-colon in the description > line) and its subsequent tests on the file then fail. > Sadly, PIR is not a subformat of FASTA ... it was the format used for the NBRF/PIR sequence analysis package. It has other odd features, not all of which are strictly used by EMBOSS (because most can be safely ignored :-) regards, Peter Rice From Fei.Zhong at qiagen.com Wed Jul 21 15:48:49 2004 From: Fei.Zhong at qiagen.com (Fei.Zhong at qiagen.com) Date: Wed, 21 Jul 2004 11:48:49 -0400 Subject: [EMBOSS] need help! Message-ID: Hello, I would like to use one tool, palindrome of EMBOSS. I downloaded the package EMBOSS-2.9.0.tar.gz and installed the whole package in my computer following the installation instruction. My computer OS is Sun Solaris Unix 9.0. I did not see any error message or special warning when I installed it. But while I try to run it, I got a problem. The error message is listed as follows: 54 fzhong at sirna:/export/home/fzhong/test/arrayProbe>/usr/local/bin/EMBOSS/b in/bin/palindrome ld.so.1: /usr/local/bin/EMBOSS/bin/bin/palindrome: fatal: libgcc_s.so.1: open failed: No such file or directory Killed Thanks so much in advance, Fei -------------- next part -------------- An HTML attachment was scrubbed... URL: From Paul.Baumgartner at unibas.ch Thu Jul 22 15:27:19 2004 From: Paul.Baumgartner at unibas.ch (Paul Baumgartner) Date: Thu, 22 Jul 2004 17:27:19 +0200 Subject: [EMBOSS] weekday Message-ID: <9E902D94-DBF3-11D8-BD8F-003065B9531E@unibas.ch> Dear all fuzznuc seems to calculate the weekday wrong Output report [stdout]: ######################################## # Program: fuzznuc # Rundate: Sun Jul 22 16:08:24 2004 # Report_format: seqtable # Report_file: stdout ######################################## see rundate. Using 2.8.0 on macosx 10.3.4 thanks Paul Biozentrum Paul Baumgartner Zellbiologie Klingelbergstrasse 70 CH-4056 Basel From d.gatherer at vir.gla.ac.uk Fri Jul 23 09:52:11 2004 From: d.gatherer at vir.gla.ac.uk (Derek Gatherer) Date: Fri, 23 Jul 2004 10:52:11 +0100 Subject: [EMBOSS] incorporating old code in 2.9.0 Message-ID: <5.2.1.1.1.20040723083507.02dd7650@udcf.gla.ac.uk> Hi I have some local legacy code (written by a predecessor around 2000), which was successfully incorporated in 2.8.0. I used to get the CVS version of EMBOSS, stick the local *.c and *.acd in the relevant places, modify the Makefile.am, then run aclocal -I m4, autoconf -v, automake -a and then a configure, make and make install as usual. However, the old code is now failing at make with 2.9.0. The errors are slightly different for each but all are incompatible types in assignment. For instance, with one I get: incompatible type for argument 2 of `ajSeqReplace' and another: incompatible type for argument 1 of `ajStrChar' Is this because something has changed in nucleus/ajax etc which precludes the use of the old code? The only other thing that I think might be relevant is that I've recently upgraded my compiler to gcc-3.3.2, from a seriously old version. I'm still using autoconf-2.57 and automake-1.7.5. I can provide further details if this is not enough to diagnose. Cheers Derek _________________________ Derek Gatherer Ph.D. Cert.Ed. Computer Officer Institute of Virology Church St. Glasgow G11 5JR Phone: +44 141 330 6268 Fax: +44 141 337 2236 Email: d.gatherer at vir.gla.ac.uk Website: http://www.vir.gla.ac.uk From pmr at ebi.ac.uk Fri Jul 23 10:29:54 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 23 Jul 2004 11:29:54 +0100 Subject: [EMBOSS] incorporating old code in 2.9.0 In-Reply-To: <5.2.1.1.1.20040723083507.02dd7650@udcf.gla.ac.uk> References: <5.2.1.1.1.20040723083507.02dd7650@udcf.gla.ac.uk> Message-ID: <4100E8A2.70302@ebi.ac.uk> Derek Gatherer wrote: > However, the old code is now failing at make with 2.9.0. The errors are > slightly different for each but all are incompatible types in assignment. > > For instance, with one I get: > > incompatible type for argument 2 of `ajSeqReplace' > > and another: > > incompatible type for argument 1 of `ajStrChar' > > Is this because something has changed in nucleus/ajax etc which > precludes the use of the old code? Curious that you get errors. Passing an AjPStr to these functions should be fine. If you send me an example program it should be easy to fix. In cleaning up the code for 2.9.0 we have become strict about defining "const AjPStr" and "const char*" for read-only parameters. You may see some messages about return types - functions will now return a "const AjPStr" or a "const char*" which can cause you problems if you assign them to a non-const variable. Usually, copying them allows you to fix code easily. Tehre were some issues with the EMBOSS code, but nobody else using the current CVS code reported difficulties while we were nitroducing the changes. In the case of these two functions, the prototypes are now: void ajSeqReplace (AjPSeq thys, const AjPStr seq); char ajStrChar (const AjPStr thys, ajint pos); One issue is that the definition of AjPStr itself had to change to be a macro, so perhaps there is something strange with your include files or dependencies. AjPStr was part of the "typedef" for strings, but somehow compilers all fail to understand "const AjPStr" (they made the pointer constant) so it is now a macro that translates to "AjOStr*" and that means "const AjPStr" translates to "const AjOStr*" which is understood correctly by compilers (they make the string constant - strictly, they make the next level of the structure constant, which is all C compilers can do). By the way - we will all be in Glasgow next week for BOSC and ISMB - I expect we will see you there? regards, Peter Rice From kvddrift at earthlink.net Fri Jul 23 10:32:20 2004 From: kvddrift at earthlink.net (Koen van der Drift) Date: Fri, 23 Jul 2004 06:32:20 -0400 Subject: [EMBOSS] emboss, rebase and fink Message-ID: <93B17242-DC93-11D8-8F60-003065A5FDCC@earthlink.net> Hi, From an fink/emboss user I got a request to make a fink-package for rebase that will install the files proto and withrefm using rebaseextract. I got this all to work, but rebaseextract installs the files directly into the main fink tree, instead of in the fink required location where packages are built. So I need to patch the code for the package to be submitted to fink. I checked rebaseextract.c (and ajFile.c) and found that the location where rebaseextract puts the file is more or less hard-coded into the emboss code. Is there a way I can manipulate this location for the fink package, eg by replacing the calls to ajFileDataNewWrite() with one that accepts a user defined location? thanks, - Koen. From pmr at ebi.ac.uk Fri Jul 23 11:14:57 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 23 Jul 2004 12:14:57 +0100 Subject: [EMBOSS] incorporating old code in 2.9.0 In-Reply-To: <5.2.1.1.1.20040723115152.02dd6770@udcf.gla.ac.uk> References: <5.2.1.1.1.20040723083507.02dd7650@udcf.gla.ac.uk> <5.2.1.1.1.20040723083507.02dd7650@udcf.gla.ac.uk> <5.2.1.1.1.20040723115152.02dd6770@udcf.gla.ac.uk> Message-ID: <4100F331.5080002@ebi.ac.uk> Derek Gatherer wrote: (see Derek's previous message to emboss at embnet.org for the problem - copied to emboss-dev because developers will need to know the answer). Solution: All variable declarations of the type: AjPStr astr, bstr; must be split into single variables from EMBOSS 2.9.0: AjPStr astr; AjPStr bstr; Explanation follows. > Hi Peter > > Here is the full error set for one of the apps: > > compact.c: In function `main': > compact.c:53: error: incompatible types in assignment > > and the code is attached. > > #include "emboss.h" > int main (int argc, char **argv) > { > AjPStr cseq, cseqo; > cseq = ajStrNew(); > cseqo = ajStrNew(); Ah, all is now clear. I just kept the relevant lines included above. Note that the cseq line is fine, the cseqo line is the one that gives the error. The cause is the redefinition of AjPStr as a macro to make "const AjPStr" work. Sorry, I forgot to stress this one in the release notes. The problem is the line: AjPStr cseq, cseqo; Because AjPStr is now a macro that is replaced by "const AjOStr*" the definition of cseqo becomes: const AjOStr* cseq, cseqo; This is a classic C problem - cseq is now an AjPStr, cseqo is only an AjOStr (what an AjPStr points to). The solution ... AjPStr cseq; AjPStr cseqo; All AjP definitions have to now be one per line. Sorry - we worked very hard to avouid this, but the compilers simply fail to put the const in the right place otherwise so we have to live with the macro and this side effect. This should solve your problems. regards, Peter Rice From jrvalverde at cnb.uam.es Fri Jul 23 12:27:51 2004 From: jrvalverde at cnb.uam.es (=?ISO-8859-15?Q?Jos=E9?= R. Valverde) Date: Fri, 23 Jul 2004 14:27:51 +0200 Subject: [EMBOSS] incorporating old code in 2.9.0 In-Reply-To: <4100F331.5080002@ebi.ac.uk> References: <5.2.1.1.1.20040723083507.02dd7650@udcf.gla.ac.uk> <5.2.1.1.1.20040723083507.02dd7650@udcf.gla.ac.uk> <5.2.1.1.1.20040723115152.02dd6770@udcf.gla.ac.uk> <4100F331.5080002@ebi.ac.uk> Message-ID: <20040723142751.628764c8.jrvalverde@cnb.uam.es> > Because AjPStr is now a macro that is replaced by "const AjOStr*" the > definition of cseqo becomes: > > const AjOStr* cseq, cseqo; > > This is a classic C problem - cseq is now an AjPStr, cseqo is only an AjOStr > (what an AjPStr points to). > Excuse me, but I've got a doubt regarding this. Wouldn't typedef const AjOStr * AjPStr; fix this and allow for multiple declarations in the same line? j -- These opinions are mine and only mine. Hey man, I saw them first! Jos? R. Valverde De nada sirve la Inteligencia Artificial cuando falta la Natural From justbeforeme at hotmail.com Mon Jul 26 03:51:38 2004 From: justbeforeme at hotmail.com (kenix y) Date: Mon, 26 Jul 2004 11:51:38 +0800 Subject: [EMBOSS] error in ajacd.c Message-ID: Hi, When I try to run any emboss application, I got the following error: error while loading shared libraries: libnucleus.so.0: cannot open shared object file: no such file or directory. But the file is located at /opt/BioBrew/EMBOSS/2.6.0/lib/ After I tried to set up the environment for using EMBOSS in ~/.bashrc export LD_LIBRARY_PATH=/opt/BioBrew/EMBOSS/2.6.0/lib:$LD_LIBRARY_PATH the error changed to EMBOSS An error in ajacd.c at line 1534: acdfile '/home/build/BuildRoot-ia32/BUILD/EMBOSS-2.6.0/emboss/acd/wossname.acd' not opened. Does anyone knows how to solve this? Thank you Rgds, kenix _________________________________________________________________ Get 10mb of inbox space with MSN Hotmail Extra Storage http://join.msn.com/?pgmarket=en-sg From Bent.Terp at biosci.ki.se Mon Jul 26 06:26:52 2004 From: Bent.Terp at biosci.ki.se (Bent Terp) Date: Mon, 26 Jul 2004 08:26:52 +0200 Subject: [EMBOSS] error in ajacd.c In-Reply-To: References: Message-ID: <1090823212.8703.2.camel@latte> On Mon, 2004-07-26 at 05:51, kenix y wrote: > Hi, > > When I try to run any emboss application, I got the following error: > error while loading shared libraries: libnucleus.so.0: cannot open shared > object file: no such file or directory. > But the file is located at /opt/BioBrew/EMBOSS/2.6.0/lib/ > > After I tried to set up the environment for using EMBOSS in ~/.bashrc > export LD_LIBRARY_PATH=/opt/BioBrew/EMBOSS/2.6.0/lib:$LD_LIBRARY_PATH > > the error changed to > EMBOSS An error in ajacd.c at line 1534: acdfile > '/home/build/BuildRoot-ia32/BUILD/EMBOSS-2.6.0/emboss/acd/wossname.acd' not > opened. > > Does anyone knows how to solve this? You need your environment set up as in the installation docs. Basically add this to your .bashrc: declare -x EMBOSS_ACDROOT="/usr/share/EMBOSS/acd" declare -x EMBOSS_DATA="/usr/share/EMBOSS/data" declare -x EMBOSS_DATABASE_DIR="/usr/share/EMBOSS/data" declare -x EMBOSS_DOCROOT="/usr/share/EMBOSS/doc" substituting /opt/BioBrew/EMBOSS for /usr/share/EMBOSS alternatively, if you're using redhat, you can install EMBOSS through declare -x EMBOSS_DATA="/usr/share/EMBOSS/data" >declare -x EMBOSS_DATABASE_DIR="/usr/share/EMBOSS/data" >declare -x EMBOSS_DOCROOT="/usr/share/EMBOSS/doc" I find them in /opt/BioBrew/EMBOSS/2.6.0/share/EMBOSS Should the paths be changed to >declare -x EMBOSS_ACDROOT="/opt/BioBrew/EMBOSS/2.6.0/share/EMBOSS/acd" >declare -x EMBOSS_DATA="/opt/BioBrew/EMBOSS/2.6.0/share/EMBOSS/data" >declare -x >EMBOSS_DATABASE_DIR="/opt/BioBrew/EMBOSS/2.6.0/share/EMBOSS/data" >declare -x EMBOSS_DOCROOT="/opt/BioBrew/EMBOSS/2.6.0/share/EMBOSS/doc" in my case? Thank you. >From: Bent Terp >To: EMBOSS list >Subject: Re: [EMBOSS] error in ajacd.c >Date: Mon, 26 Jul 2004 08:26:52 +0200 > >On Mon, 2004-07-26 at 05:51, kenix y wrote: > > Hi, > > > > When I try to run any emboss application, I got the following error: > > error while loading shared libraries: libnucleus.so.0: cannot open >shared > > object file: no such file or directory. > > But the file is located at /opt/BioBrew/EMBOSS/2.6.0/lib/ > > > > After I tried to set up the environment for using EMBOSS in ~/.bashrc > > export LD_LIBRARY_PATH=/opt/BioBrew/EMBOSS/2.6.0/lib:$LD_LIBRARY_PATH > > > > the error changed to > > EMBOSS An error in ajacd.c at line 1534: acdfile > > '/home/build/BuildRoot-ia32/BUILD/EMBOSS-2.6.0/emboss/acd/wossname.acd' >not > > opened. > > > > Does anyone knows how to solve this? > >You need your environment set up as in the installation docs. Basically >add this to your .bashrc: >declare -x EMBOSS_ACDROOT="/usr/share/EMBOSS/acd" >declare -x EMBOSS_DATA="/usr/share/EMBOSS/data" >declare -x EMBOSS_DATABASE_DIR="/usr/share/EMBOSS/data" >declare -x EMBOSS_DOCROOT="/usr/share/EMBOSS/doc" > >substituting /opt/BioBrew/EMBOSS for /usr/share/EMBOSS > > alternatively, if you're using redhat, you can >install EMBOSS through >declare -x EMBOSS_DATA="/usr/share/EMBOSS/data" > >declare -x EMBOSS_DATABASE_DIR="/usr/share/EMBOSS/data" > >declare -x EMBOSS_DOCROOT="/usr/share/EMBOSS/doc" > > I find them in /opt/BioBrew/EMBOSS/2.6.0/share/EMBOSS > > Should the paths be changed to > >declare -x EMBOSS_ACDROOT="/opt/BioBrew/EMBOSS/2.6.0/share/EMBOSS/acd" > >declare -x EMBOSS_DATA="/opt/BioBrew/EMBOSS/2.6.0/share/EMBOSS/data" > >declare -x > >EMBOSS_DATABASE_DIR="/opt/BioBrew/EMBOSS/2.6.0/share/EMBOSS/data" > >declare -x EMBOSS_DOCROOT="/opt/BioBrew/EMBOSS/2.6.0/share/EMBOSS/doc" > > in my case? If you have a dir called /opt/BioBrew/EMBOSS/2.6.0/share/EMBOSS/acd then yes Out of sheer curiosity, what else have you got installed in /opt/BioBrew? Merely interested to know of other apps I should add to BioRPMS.... > > Thank you. > > >From: Bent Terp > >To: EMBOSS list > >Subject: Re: [EMBOSS] error in ajacd.c > >Date: Mon, 26 Jul 2004 08:26:52 +0200 > > > >On Mon, 2004-07-26 at 05:51, kenix y wrote: > > > Hi, > > > > > > When I try to run any emboss application, I got the following error: > > > error while loading shared libraries: libnucleus.so.0: cannot open > >shared > > > object file: no such file or directory. > > > But the file is located at /opt/BioBrew/EMBOSS/2.6.0/lib/ > > > > > > After I tried to set up the environment for using EMBOSS in ~/.bashrc > > > export LD_LIBRARY_PATH=/opt/BioBrew/EMBOSS/2.6.0/lib:$LD_LIBRARY_PATH > > > > > > the error changed to > > > EMBOSS An error in ajacd.c at line 1534: acdfile > > > '/home/build/BuildRoot-ia32/BUILD/EMBOSS-2.6.0/emboss/acd/wossname.acd' > >not > > > opened. > > > > > > Does anyone knows how to solve this? > > > >You need your environment set up as in the installation docs. Basically > >add this to your .bashrc: > >declare -x EMBOSS_ACDROOT="/usr/share/EMBOSS/acd" > >declare -x EMBOSS_DATA="/usr/share/EMBOSS/data" > >declare -x EMBOSS_DATABASE_DIR="/usr/share/EMBOSS/data" > >declare -x EMBOSS_DOCROOT="/usr/share/EMBOSS/doc" > > > >substituting /opt/BioBrew/EMBOSS for /usr/share/EMBOSS > > > > alternatively, if you're using redhat, you can > >install EMBOSS through References: <4100E8A2.70302@ebi.ac.uk> <5.2.1.1.1.20040723083507.02dd7650@udcf.gla.ac.uk> <5.2.1.1.1.20040723083507.02dd7650@udcf.gla.ac.uk> Message-ID: <5.2.1.1.1.20040726102546.02dff1c0@udcf.gla.ac.uk> and the same applies to AjPFloat, ie: AjPFloat matrixa; AjPFloat matrixb; AjPFloat matrixc; AjPFloat matrixe; is necessary. At 09:56 26/07/2004 +0100, Derek Gatherer wrote: >At 11:29 23/07/2004 +0100, Peter Rice wrote: > >>In cleaning up the code for 2.9.0 we have become strict about defining >>"const AjPStr" and "const char*" for read-only parameters. > >It seems that AjPFile variable also need to be declared one line at a time >too. Eg: > >This compiles okay: > >int main (int argc, char **argv) >{ > AjPFile fhmatina; // all AjPFile need own lines for 2.9.0 > AjPFile fhmatinb; > AjPFile fhoutmat; > AjPStr linea; // all AjPStr need own lines for 2.9.0 > AjPStr lineb; > AjPStr elementa; > AjPStr elementb; > ajint i, j, seqsina, seqsinb; > float ftmpa, ftmpb, sigmax2=0, sigmax=0, xsigmax2=0, xsigmax=0; > float mean, xmean, sdsample, sdpopulation, xsdsample, xsdpopulation; > float gbrate; > char *ctmp; > >but this crashes at make with the same "incompatible types in assignment" >error. > >int main (int argc, char **argv) >{ > AjPFile fhmatina, fhmatinb, fhoutmat; > AjPStr linea; // all AjPStr need own lines for 2.9.0 > AjPStr lineb; > AjPStr elementa; > AjPStr elementb; > ajint i, j, seqsina, seqsinb; > float ftmpa, ftmpb, sigmax2=0, sigmax=0, xsigmax2=0, xsigmax=0; > float mean, xmean, sdsample, sdpopulation, xsdsample, xsdpopulation; > float gbrate; > char *ctmp; > >I'm still making, so if I find anything else, I'll let you know. I'm >about halfway through make, and so far this is the only additional error. > >cheers >Derek >_________________________ > >Derek Gatherer Ph.D. Cert.Ed. >Computer Officer >Institute of Virology >Church St. >Glasgow G11 5JR > >Phone: +44 141 330 6268 >Fax: +44 141 337 2236 >Email: d.gatherer at vir.gla.ac.uk >Website: http://www.vir.gla.ac.uk _________________________ Derek Gatherer Ph.D. Cert.Ed. Computer Officer Institute of Virology Church St. Glasgow G11 5JR Phone: +44 141 330 6268 Fax: +44 141 337 2236 Email: d.gatherer at vir.gla.ac.uk Website: http://www.vir.gla.ac.uk From bobby_rgm at yahoo.com Wed Jul 28 11:34:08 2004 From: bobby_rgm at yahoo.com (chowdary manio) Date: Wed, 28 Jul 2004 04:34:08 -0700 (PDT) Subject: [EMBOSS] protein sequence input Message-ID: <20040728113408.58345.qmail@web53207.mail.yahoo.com> hi, I am using the emboss to make protein sequence analysis. I want the program "water"(smith-waterman algorithm) to take in the characters "J","O","U" which are not aminoacid symbols. Can I change the code?, If so, in which file I have to make this change, to make the program take this desired input Thank you, bobby __________________________________ Do you Yahoo!? New and Improved Yahoo! Mail - 100MB free storage! http://promotions.yahoo.com/new_mail From pmr at ebi.ac.uk Wed Jul 28 14:13:37 2004 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Wed, 28 Jul 2004 15:13:37 +0100 (BST) Subject: [EMBOSS] protein sequence input In-Reply-To: <20040728113408.58345.qmail@web53207.mail.yahoo.com> References: <20040728113408.58345.qmail@web53207.mail.yahoo.com> Message-ID: <40552.217.45.210.49.1091024017.squirrel@webmail.ebi.ac.uk> Hi Bobby, > I am using the emboss to make protein sequence > analysis. > > I want the program "water"(smith-waterman algorithm) > to take in the characters "J","O","U" which are not > aminoacid symbols. > > Can I change the code?, If so, in which file I have to > make this change, to make the program take this > desired input Interesting question. The sequence types are checked in ajax/ajseqtype.c But there is also the question of whether your sequence is really a protein. Perhaps we should allow "alpha" as a sequence type, with its own comparison matrices. It could get complicated (we need to check whether we assume all non-nucleic sequences are protein, for example). "U" is a valid protein code (for selenocysteine). "O" is used as a gap character by some formats. "J" is not used. I have seen "O" and "J" used in modified matrices before - though that was as DNA to score CpG islands differently (CG was converted to OJ and given higher match scores) Perhaps, as a quick solution, you could try using the protein ambiguity codes B and Z instead of O and J? Then you could use a normal protein sequence. Hope that helps, Peter