From Veronique.Martin at jouy.inra.fr Tue Nov 4 09:35:14 2008 From: Veronique.Martin at jouy.inra.fr (Veronique.Martin at jouy.inra.fr) Date: Tue, 4 Nov 2008 15:35:14 +0100 (CET) Subject: [EMBOSS] fuzznuc option report Message-ID: Hi all, With fuzznuc how can I get in the report, the total sequences that there are in my sequence list. At the end of the report, there is just the total of sequences found by fuzznuc and the total hitcount, but I would like to known, how many sequence was in my list at the begining. In the following example my sequence list was 50 sequences. #--------------------------------------- # Total_sequences: 40 # Total_hitcount: 44 #--------------------------------------- Is it possible to have something like that? ------------------------------------------- Total finds: 40 Total hitcount: 44 Total sequences: 50 -------------------------------------------- Thanks and regards, Veronique ------------------------------------------------- V?ronique MARTIN INRA - Unit? Math?matique, Informatique et G?nome 78352 Jouy-en Josas cedex tel.: 01 34 65 29 74 ------------------------------------------------- From pmr at ebi.ac.uk Tue Nov 4 10:30:34 2008 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 04 Nov 2008 15:30:34 +0000 Subject: [EMBOSS] fuzznuc option report In-Reply-To: References: Message-ID: <49106A9A.9010103@ebi.ac.uk> Veronique.Martin at jouy.inra.fr wrote: > With fuzznuc how can I get in the report, the total sequences that there > are in my sequence list. > > At the end of the report, there is just the total of sequences found by > fuzznuc and the total hitcount, but I would like to known, how many > sequence was in my list at the begining. > In the following example my sequence list was 50 sequences. > > #--------------------------------------- > # Total_sequences: 40 > # Total_hitcount: 44 > #--------------------------------------- > > Is it possible to have something like that? > ------------------------------------------- > Total finds: 40 > Total hitcount: 44 > Total sequences: 50 > -------------------------------------------- Interesting question. It is more difficult than it seems. In the current output, "Total_sequences" is the number of times the report output has been called. Fuzznuc (and other programs) only call report output functions when they have something to report. Only the calling program (fuzznuc) knows how many sequences were read. However, the tail is written when the report file is closed, so we can simply pass the total number of input sequences to a version of ajReportClose, or add a function that sets a value for the report tail. We will add it to the next release. regards, Peter Rice From jison at ebi.ac.uk Tue Nov 4 10:34:02 2008 From: jison at ebi.ac.uk (Jon Ison) Date: Tue, 4 Nov 2008 15:34:02 -0000 (GMT) Subject: [EMBOSS] fuzznuc option report In-Reply-To: References: Message-ID: <56691.84.92.187.247.1225812842.squirrel@webmail.ebi.ac.uk> Hi Veronique The short answer is currently you can't. It would be easy to change the report and application code though (will discuss at next EMBOSS meeting). Cheers Jon > > Hi all, > > With fuzznuc how can I get in the report, the total sequences that there > are in my sequence list. > > At the end of the report, there is just the total of sequences found by > fuzznuc and the total hitcount, but I would like to known, how many > sequence was in my list at the begining. > In the following example my sequence list was 50 sequences. > > #--------------------------------------- > # Total_sequences: 40 > # Total_hitcount: 44 > #--------------------------------------- > > Is it possible to have something like that? > ------------------------------------------- > Total finds: 40 > Total hitcount: 44 > Total sequences: 50 > -------------------------------------------- > > Thanks and regards, > > Veronique > > ------------------------------------------------- > V?ronique MARTIN > INRA - Unit? Math?matique, Informatique et G?nome > 78352 Jouy-en Josas cedex > tel.: 01 34 65 29 74 > -------------------------------------------------_______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From db60 at st-andrews.ac.uk Tue Nov 4 11:00:26 2008 From: db60 at st-andrews.ac.uk (Daniel Barker) Date: Tue, 04 Nov 2008 16:00:26 +0000 Subject: [EMBOSS] fuzznuc option report In-Reply-To: <56691.84.92.187.247.1225812842.squirrel@webmail.ebi.ac.uk> References: <56691.84.92.187.247.1225812842.squirrel@webmail.ebi.ac.uk> Message-ID: <4910719A.4050003@st-andrews.ac.uk> >> With fuzznuc how can I get in the report, the total sequences >> that there are in my sequence list. If your sequences are in Fasta format, it's not too difficult to count sequences as separate step, prior to running the program, e.g. on Linux or OS X: grep -c '>' seqfile.fa Remember the single quotes, or else it won't work and even worse, you'll delete all sequences in the sequence file! Best wishes, Daniel -- Daniel Barker http://bio.st-andrews.ac.uk/staff/db60.htm The University of St Andrews is a charity registered in Scotland : No SC013532 From Perdeep.Mehta at STJUDE.ORG Tue Nov 4 12:08:03 2008 From: Perdeep.Mehta at STJUDE.ORG (Mehta, Perdeep) Date: Tue, 4 Nov 2008 11:08:03 -0600 Subject: [EMBOSS] extracting sequence from a pdb file In-Reply-To: References: Message-ID: <6EAE916704479E4BB6AB5A133BA224F70247E53D69@SJMEMXMBS11.stjude.sjcrh.local> Hi, Does anyone know if there is a program in EMBOSS that can extract protein sequence from a pdb format file? thanks, perdeep Perdeep K. Mehta, PhD Research Informatics, Information Sciences Division St. Jude Children's Research Hospital 262 Danny Thomas Place Memphis, TN 38105-2794 Tel: 901-495 3774 http://www.hatwellcenter.org/ From pmr at ebi.ac.uk Tue Nov 4 13:03:31 2008 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 04 Nov 2008 18:03:31 +0000 Subject: [EMBOSS] extracting sequence from a pdb file In-Reply-To: <6EAE916704479E4BB6AB5A133BA224F70247E53D69@SJMEMXMBS11.stjude.sjcrh.local> References: <6EAE916704479E4BB6AB5A133BA224F70247E53D69@SJMEMXMBS11.stjude.sjcrh.local> Message-ID: <49108E73.5030500@ebi.ac.uk> Mehta, Perdeep wrote: > Hi, > > Does anyone know if there is a program in EMBOSS that can extract protein sequence from a pdb format file? It depends on the pdb file format. There is a "pdb" sequence format that reads from the ATOM records, but fails on some pdb entries. There is also a "pdbseq" sequence format (-sf pdbseq on the command line) that reads the SEQRES records. If you find a PDB file that fails to read, please let us know. I just tested on an old 2ins entry file and it found zero sequences and failed (it was designed for a cleaned up PDB format). regards, Peter Rice From Perdeep.Mehta at STJUDE.ORG Tue Nov 4 15:42:40 2008 From: Perdeep.Mehta at STJUDE.ORG (Mehta, Perdeep) Date: Tue, 4 Nov 2008 14:42:40 -0600 Subject: [EMBOSS] extracting sequence from a pdb file In-Reply-To: <49108E73.5030500@ebi.ac.uk> References: <6EAE916704479E4BB6AB5A133BA224F70247E53D69@SJMEMXMBS11.stjude.sjcrh.local> <49108E73.5030500@ebi.ac.uk> Message-ID: <6EAE916704479E4BB6AB5A133BA224F70247E53D6A@SJMEMXMBS11.stjude.sjcrh.local> Thanks Peter. The file is standard ATOM record straight from PDB. I will check on that. Best regards, perdeep -----Original Message----- From: Peter Rice [mailto:pmr at ebi.ac.uk] Sent: Tuesday, November 04, 2008 12:04 PM To: emboss at emboss.open-bio.org Cc: Mehta, Perdeep Subject: Re: [EMBOSS] extracting sequence from a pdb file Mehta, Perdeep wrote: > Hi, > > Does anyone know if there is a program in EMBOSS that can extract protein sequence from a pdb format file? It depends on the pdb file format. There is a "pdb" sequence format that reads from the ATOM records, but fails on some pdb entries. There is also a "pdbseq" sequence format (-sf pdbseq on the command line) that reads the SEQRES records. If you find a PDB file that fails to read, please let us know. I just tested on an old 2ins entry file and it found zero sequences and failed (it was designed for a cleaned up PDB format). regards, Peter Rice From jison at ebi.ac.uk Wed Nov 5 07:24:28 2008 From: jison at ebi.ac.uk (Jon Ison) Date: Wed, 5 Nov 2008 12:24:28 -0000 (GMT) Subject: [EMBOSS] extracting sequence from a pdb file In-Reply-To: <6EAE916704479E4BB6AB5A133BA224F70247E53D69@SJMEMXMBS11.stjude.sjcrh.l ocal> References: <6EAE916704479E4BB6AB5A133BA224F70247E53D69@SJMEMXMBS11.stjude.sjcrh.local> Message-ID: <47987.84.92.187.247.1225887868.squirrel@webmail.ebi.ac.uk> Hi Perdeep You can use the program pdbparse from the "structure" EMBASSY package: http://emboss.sourceforge.net/apps/cvs/embassy/structure/ It will read ATOM / SEQRES records and write the true (corrected) molecular sequence (which is not an easy task!) to a file in a "clean" (easy to parse) format, which other EMBASSY packages can then make use of. There are various options for controlling how it handles e.g. missing atoms, mismatches, non-amino acid groups etc. in the original file. It's been a long while since I tested the program on the whole of PDB though so there are probably files it will fail for. If you need to extract the sequence into any specified sequence format then we could write a program for that (or something else) for the next release. Let me know. Cheers Jon > Hi, > > Does anyone know if there is a program in EMBOSS that can extract protein sequence from a pdb format file? > > thanks, > perdeep > > Perdeep K. Mehta, PhD > Research Informatics, Information Sciences Division > St. Jude Children's Research Hospital > 262 Danny Thomas Place > Memphis, TN 38105-2794 > Tel: 901-495 3774 > http://www.hatwellcenter.org/ > > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From mahvash.khalid at gmail.com Mon Nov 10 03:36:08 2008 From: mahvash.khalid at gmail.com (Mahvash Khalid) Date: Mon, 10 Nov 2008 13:36:08 +0500 Subject: [EMBOSS] (no subject) Message-ID: <67c424ae0811100036k40691baal500288fd0f7ac64e@mail.gmail.com> hiii.. iam a bioinformatics student and workin in linux .. my project is on coxepression of genes in humans ... but i dont know much abt java.. as java is the language which linux supports and not csharp.. i wanted to compare the start of mrna and coding regions to check the presence or absence of TSS ... if anyone can help i will be really grateful.. thanks mahvash From uludag at ebi.ac.uk Wed Nov 12 11:38:56 2008 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Wed, 12 Nov 2008 16:38:56 +0000 Subject: [EMBOSS] (no subject) In-Reply-To: <67c424ae0811100036k40691baal500288fd0f7ac64e@mail.gmail.com> References: <67c424ae0811100036k40691baal500288fd0f7ac64e@mail.gmail.com> Message-ID: <1226507936.21078.110.camel@emboss2.ebi.ac.uk> Hi Mahvash, > iam a bioinformatics student and workin in linux .. my project is on > coxepression of genes in humans ... but i dont know much abt java.. as java > is the language which linux supports and not csharp.. > i wanted to compare the start of mrna and coding regions to check the > presence or absence of TSS ... I talked to a colleague from the EBI RNA genomics group about your question. Harpreet told me you can do these comparisons using the Ensembl web site. I now forward your message to Harpreet. (If she can't post her answer to the emboss list, as she is not a member on the list, I will try posting on her behalf) Regards, Mahmut > if anyone can help i will be really grateful.. > thanks > mahvash From uludag at ebi.ac.uk Wed Nov 12 12:22:28 2008 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Wed, 12 Nov 2008 17:22:28 +0000 Subject: [EMBOSS] (no subject) In-Reply-To: <0A718E3F-2293-4567-B1AB-8C37211D4545@ebi.ac.uk> References: <67c424ae0811100036k40691baal500288fd0f7ac64e@mail.gmail.com> <1226507936.21078.110.camel@emboss2.ebi.ac.uk> <0A718E3F-2293-4567-B1AB-8C37211D4545@ebi.ac.uk> Message-ID: <1226510548.21078.138.camel@emboss2.ebi.ac.uk> If anyone else on the list is also interested to know how to get TSS information using Ensembl I forward Harpreet's message below. Harpreet told me "Eponine regions" feature should be used to get TSS information for Humans. Regards, Mahmut On Wed, 2008-11-12 at 16:46 +0000, Harpreet Saini wrote: > Hi Mahvash, > > I have used Ensembl web site many times to get the information about > the transcription start sites (TSS). You can get the TSS from the > features link in the Ensembl genome browser for your organism of > interest. > The other thing is that you can also easily obtain the start/end of > mRNA and coding regions from the Ensembl database using the Perl API. > If you have not used Ensembl or perl API before, then the ensembl web > site have very nice tutorials for beginners. > > Hope this will help you. > > Regards > Harpreet > > On 12 Nov 2008, at 16:38, Mahmut Uludag wrote: > > > Hi Mahvash, > > > >> iam a bioinformatics student and workin in linux .. my project is on > >> coxepression of genes in humans ... but i dont know much abt java.. > >> as java > >> is the language which linux supports and not csharp.. > >> i wanted to compare the start of mrna and coding regions to check the > >> presence or absence of TSS ... > > > > I talked to a colleague from the EBI RNA genomics group about your > > question. Harpreet told me you can do these comparisons using the > > Ensembl web site. I now forward your message to Harpreet. (If she > > can't > > post her answer to the emboss list, as she is not a member on the > > list, > > I will try posting on her behalf) > > > > Regards, > > Mahmut > > > >> if anyone can help i will be really grateful.. > >> thanks > >> mahvash > > > > Harpreet Kaur Saini > Enright Group > EMBL-European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD > Tel: +44-(0) 1223-492676 > > > > From db60 at st-andrews.ac.uk Wed Nov 12 12:55:45 2008 From: db60 at st-andrews.ac.uk (Daniel Barker) Date: Wed, 12 Nov 2008 17:55:45 +0000 Subject: [EMBOSS] (no subject) In-Reply-To: <1226510548.21078.138.camel@emboss2.ebi.ac.uk> References: <67c424ae0811100036k40691baal500288fd0f7ac64e@mail.gmail.com> <1226507936.21078.110.camel@emboss2.ebi.ac.uk> <0A718E3F-2293-4567-B1AB-8C37211D4545@ebi.ac.uk> <1226510548.21078.138.camel@emboss2.ebi.ac.uk> Message-ID: <491B18A1.7060000@st-andrews.ac.uk> Dear Mahmut, The Eponine regions would be TSS predicted by the Eponine program. This is different from the Ensembl Perl API approach Harpreet mentioned (e.g. use the API to get each Ensembl mRNA and see if its predicted start codon is at the beginning or not). It's fair to say both approaches will get you predictions, but different ones, due to different methodology used to generate the predictions. Best wishes, Daniel. Mahmut Uludag wrote: > If anyone else on the list is also interested to know how to get TSS > information using Ensembl I forward Harpreet's message below. Harpreet > told me "Eponine regions" feature should be used to get TSS information > for Humans. > > Regards, > Mahmut > > > On Wed, 2008-11-12 at 16:46 +0000, Harpreet Saini wrote: >> Hi Mahvash, >> >> I have used Ensembl web site many times to get the information about >> the transcription start sites (TSS). You can get the TSS from the >> features link in the Ensembl genome browser for your organism of >> interest. >> The other thing is that you can also easily obtain the start/end of >> mRNA and coding regions from the Ensembl database using the Perl API. >> If you have not used Ensembl or perl API before, then the ensembl web >> site have very nice tutorials for beginners. >> >> Hope this will help you. >> >> Regards >> Harpreet >> >> On 12 Nov 2008, at 16:38, Mahmut Uludag wrote: >> >>> Hi Mahvash, >>> >>>> iam a bioinformatics student and workin in linux .. my project is on >>>> coxepression of genes in humans ... but i dont know much abt java.. >>>> as java >>>> is the language which linux supports and not csharp.. >>>> i wanted to compare the start of mrna and coding regions to check the >>>> presence or absence of TSS ... >>> I talked to a colleague from the EBI RNA genomics group about your >>> question. Harpreet told me you can do these comparisons using the >>> Ensembl web site. I now forward your message to Harpreet. (If she >>> can't >>> post her answer to the emboss list, as she is not a member on the >>> list, >>> I will try posting on her behalf) >>> >>> Regards, >>> Mahmut >>> >>>> if anyone can help i will be really grateful.. >>>> thanks >>>> mahvash >> Harpreet Kaur Saini >> Enright Group >> EMBL-European Bioinformatics Institute >> Wellcome Trust Genome Campus >> Hinxton, Cambridge >> CB10 1SD >> Tel: +44-(0) 1223-492676 >> >> >> >> > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss -- Daniel Barker http://bio.st-andrews.ac.uk/staff/db60.htm The University of St Andrews is a charity registered in Scotland : No SC013532 From sylvain.foisy at diploide.net Mon Nov 24 16:20:13 2008 From: sylvain.foisy at diploide.net (Sylvain Foisy) Date: Mon, 24 Nov 2008 16:20:13 -0500 Subject: [EMBOSS] Compiling EMBOSS: missing jni.h? Message-ID: Hi, I'am trying to build a bioinfo workstation with Xubuntu and of course, I am trying to compile the latest EMBOSS (5.0 is the latest version of the pre-built package). I just hit a snag... After invoking make, it compiles for a while and then crashes with this (sorry for the length): Making all in ajax make[1]: Entering directory `/opt/bioxubuntu/sources/EMBOSS-6.0.1/ajax' /bin/bash ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"6.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -DPLD_png=1 -I. -DAJAX_FIXED_ROOT=\"/opt/bioxubuntu/sources/EMBOSS-6.0.1/emboss\" -DPREFIX=\"/usr/local\" -I../plplot -DPOSIX_MALLOC_THRESHOLD=10 -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DLENDIAN -I/usr/lib/jvm/java-6-openjdk/jre -DHAVE_JAVA -I/usr/lib/jvm/java-6-openjdk -DNO_AUTH -O2 -MT ajacd.lo -MD -MP -MF .deps/ajacd.Tpo -c -o ajacd.lo ajacd.c mkdir .libs gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"6.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -DPLD_png=1 -I. -DAJAX_FIXED_ROOT=\"/opt/bioxubuntu/sources/EMBOSS-6.0.1/emboss\" -DPREFIX=\"/usr/local\" -I../plplot -DPOSIX_MALLOC_THRESHOLD=10 -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DLENDIAN -I/usr/lib/jvm/java-6-openjdk/jre -DHAVE_JAVA -I/usr/lib/jvm/java-6-openjdk -DNO_AUTH -O2 -MT ajacd.lo -MD -MP -MF .deps/ajacd.Tpo -c ajacd.c -fPIC -DPIC -o .libs/ajacd.o In file included from ajax.h:77, from ajacd.c:41: ajjava.h:13:17: error: jni.h: No such file or directory In file included from ajax.h:77, from ajacd.c:41: ajjava.h:33: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:35: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:38: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:41: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jint' ajjava.h:43: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jint' ajjava.h:45: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jint' ajjava.h:47: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jint' ajjava.h:50: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jint' ajjava.h:52: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jint' ajjava.h:54: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jint' ajjava.h:56: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jint' ajjava.h:60: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:67: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:71: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:75: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:79: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:83: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:87: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:91: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:96: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:101: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:106: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jbyteArray' ajjava.h:111: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:116: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:121: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' make[1]: *** [ajacd.lo] Error 1 make[1]: Leaving directory `/opt/bioxubuntu/sources/EMBOSS-6.0.1/ajax' make: *** [all-recursive] Error 1 Can anyone point me toward a solution? I have openjdk-6-jdk installed via apt-get but it seems that I am missing something... Best regards Sylvain ================================================================== Sylvain Foisy, Ph. D. Charg? de projet / Project Manager Bio-informatique Adresse postale: Laboratoire de genetique et medecine genomique de l'inflammation Institut de cardiologie de Montreal 5000 Belanger Montreal, Qc H1T 1C8 T: 514-376-3330 x.2299 | F: 514-593-2539 M: sylvain.foisy at inflammgen.org W: http://www.inflammgen.org ================================================================== From charles-listes-emboss at plessy.org Tue Nov 25 00:55:38 2008 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Tue, 25 Nov 2008 14:55:38 +0900 Subject: [EMBOSS] Compiling EMBOSS: missing jni.h? In-Reply-To: References: Message-ID: <20081125055538.GD8418@kunpuu.plessy.org> Le Mon, Nov 24, 2008 at 04:20:13PM -0500, Sylvain Foisy a ?crit : > Hi, > > I'am trying to build a bioinfo workstation with Xubuntu and of course, I am > trying to compile the latest EMBOSS (5.0 is the latest version of the > pre-built package). I just hit a snag... After invoking make, it compiles > for a while and then crashes with this (sorry for the length): Hello Sylvain, There is a Debian package ready for EMBOSS 6.0.1 in our experimental section. If you do not need jEMBOSS (that is not yet supported by our packages), you can either try to install directly the binary packages, or to compile them on your system: - Get the build tools: sudo aptitude install devscripts build-essential - Get the source package: dget -x http://ftp.de.debian.org/debian/pool/main/e/emboss/emboss_6.0.1-2.dsc - Get the build dependancies: cd emboss-6.0.1 ; sudo mk-build-deps -r -i - Make the binary packages: debuild - Install them: cd .. ; sudo dpkg -i emboss_6.0.1-2_*.deb emboss-data_6.0.1-2_all.deb emboss-doc_6.0.1-2_all.deb emboss-lib_6.0.1-2_*.deb libajax6_6.0.1-2_*.deb libnucleus6_6.0.1-2_*.deb Another way is to contact the Ubuntu MOTUs and ask them to synchronise with the Debian experimental package. The only reason why it is there is that Debian is frozen now, preparing its release. It will be part of the main distribution later (and the embassy packages will be rebuilt against it). > Can anyone point me toward a solution? I have openjdk-6-jdk installed via > apt-get but it seems that I am missing something... Have you passed the following arguments to your configure script: --with-java=/usr/lib/jvm/java-6-openjdk/include --with-javaos=/usr/lib/jvm/java-6-openjdk/include/linux Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From sylvain.foisy at diploide.net Tue Nov 25 10:22:52 2008 From: sylvain.foisy at diploide.net (Sylvain Foisy) Date: Tue, 25 Nov 2008 10:22:52 -0500 Subject: [EMBOSS] Compiling EMBOSS: missing jni.h? Message-ID: Hi, Thanks for the inputs on the paths toward java/javaos; make/make install now worked...kind of. I need the Jemboss interface to facilitate my students' interactions with EMBOSS, this is why I want to compile myself. Now the "kind of" part: I hit a "libnucleus.so.6 not found" and it seems to be related to the fact that libeplplot.so.3 is not found. I know that I have the libplplot9/libplplot-dev packages installed. Any pointers? Could I use your experimental package for emboss-libs to fix this? Thanks for the help Sylvain ================================================================== Sylvain Foisy, Ph. D. Charg? de projet / Project Manager Bio-informatique Adresse postale: Laboratoire de genetique et medecine genomique de l'inflammation Institut de cardiologie de Montreal 5000 Belanger Montreal, Qc H1T 1C8 T: 514-376-3330 x.2299 | F: 514-593-2539 M: sylvain.foisy at inflammgen.org W: http://www.inflammgen.org ================================================================== From charles-listes-emboss at plessy.org Wed Nov 26 08:17:27 2008 From: charles-listes-emboss at plessy.org (charles-listes-emboss at plessy.org) Date: Wed, 26 Nov 2008 22:17:27 +0900 Subject: [EMBOSS] Compiling EMBOSS: missing jni.h? In-Reply-To: References: Message-ID: <20081126131727.GJ21391@kunpuu.plessy.org> Le Tue, Nov 25, 2008 at 10:22:52AM -0500, Sylvain Foisy a ?crit : > > Thanks for the inputs on the paths toward java/javaos; make/make install now > worked...kind of. I need the Jemboss interface to facilitate my students' > interactions with EMBOSS, this is why I want to compile myself. > > Now the "kind of" part: I hit a "libnucleus.so.6 not found" and it seems to > be related to the fact that libeplplot.so.3 is not found. I know that I have > the libplplot9/libplplot-dev packages installed. Any pointers? Could I use > your experimental package for emboss-libs to fix this? Hi Sylvain, EMBOSS uses a fork of libplplot, that was named libeplplot to allow both libraries to be installed on the same system. (By the way, is the fork still needed?) What seems to happen on your system is that it does not find the nucleus and eplplot libraries. Although it is not really recommended to mix local and packaged installs, the packages libajax6, libnucleus6 and emboss-lib may provide you what you need. I have started to implement support for jEMBOSS in the Debian packages, but it will take time before it reaches Debian archives. What you can do if you would like to try it is to unpack the emboss sources, and within them type "debcheckout emboss". Then you can use the protocol I gave you before, with mk-build-deps if still needed, and then debuild. On my amd64 system, I just checked that something would appear whan running runJemboss, but did not verify further that it functions correctly. Lastly, if all you need is an interface, you can try the emboss-explorer package, that provides a web frontend to EMBOSS. Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From golharam at umdnj.edu Wed Nov 26 09:50:05 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Wed, 26 Nov 2008 09:50:05 -0500 Subject: [EMBOSS] Compiling EMBOSS: missing jni.h? In-Reply-To: <20081126131727.GJ21391@kunpuu.plessy.org> References: <20081126131727.GJ21391@kunpuu.plessy.org> Message-ID: <492D621D.6050104@umdnj.edu> You can obtain EMBOSS RPMs from http://informatics.umdnj.edu/BioRPMs They compile cleanly and document dependencies. charles-listes-emboss at plessy.org wrote: > Le Tue, Nov 25, 2008 at 10:22:52AM -0500, Sylvain Foisy a ?crit : >> Thanks for the inputs on the paths toward java/javaos; make/make install now >> worked...kind of. I need the Jemboss interface to facilitate my students' >> interactions with EMBOSS, this is why I want to compile myself. >> >> Now the "kind of" part: I hit a "libnucleus.so.6 not found" and it seems to >> be related to the fact that libeplplot.so.3 is not found. I know that I have >> the libplplot9/libplplot-dev packages installed. Any pointers? Could I use >> your experimental package for emboss-libs to fix this? > > Hi Sylvain, > > EMBOSS uses a fork of libplplot, that was named libeplplot to allow both > libraries to be installed on the same system. (By the way, is the fork still > needed?) What seems to happen on your system is that it does not find the > nucleus and eplplot libraries. Although it is not really recommended to mix > local and packaged installs, the packages libajax6, libnucleus6 and emboss-lib > may provide you what you need. > > I have started to implement support for jEMBOSS in the Debian packages, but it > will take time before it reaches Debian archives. What you can do if you would > like to try it is to unpack the emboss sources, and within them type > "debcheckout emboss". Then you can use the protocol I gave you before, with > mk-build-deps if still needed, and then debuild. On my amd64 system, I just > checked that something would appear whan running runJemboss, but did not verify > further that it functions correctly. > > Lastly, if all you need is an interface, you can try the emboss-explorer > package, that provides a web frontend to EMBOSS. > > Have a nice day, > -------------- next part -------------- A non-text attachment was scrubbed... Name: golharam.vcf Type: text/x-vcard Size: 439 bytes Desc: not available URL: From Veronique.Martin at jouy.inra.fr Tue Nov 4 14:35:14 2008 From: Veronique.Martin at jouy.inra.fr (Veronique.Martin at jouy.inra.fr) Date: Tue, 4 Nov 2008 15:35:14 +0100 (CET) Subject: [EMBOSS] fuzznuc option report Message-ID: Hi all, With fuzznuc how can I get in the report, the total sequences that there are in my sequence list. At the end of the report, there is just the total of sequences found by fuzznuc and the total hitcount, but I would like to known, how many sequence was in my list at the begining. In the following example my sequence list was 50 sequences. #--------------------------------------- # Total_sequences: 40 # Total_hitcount: 44 #--------------------------------------- Is it possible to have something like that? ------------------------------------------- Total finds: 40 Total hitcount: 44 Total sequences: 50 -------------------------------------------- Thanks and regards, Veronique ------------------------------------------------- V?ronique MARTIN INRA - Unit? Math?matique, Informatique et G?nome 78352 Jouy-en Josas cedex tel.: 01 34 65 29 74 ------------------------------------------------- From pmr at ebi.ac.uk Tue Nov 4 15:30:34 2008 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 04 Nov 2008 15:30:34 +0000 Subject: [EMBOSS] fuzznuc option report In-Reply-To: References: Message-ID: <49106A9A.9010103@ebi.ac.uk> Veronique.Martin at jouy.inra.fr wrote: > With fuzznuc how can I get in the report, the total sequences that there > are in my sequence list. > > At the end of the report, there is just the total of sequences found by > fuzznuc and the total hitcount, but I would like to known, how many > sequence was in my list at the begining. > In the following example my sequence list was 50 sequences. > > #--------------------------------------- > # Total_sequences: 40 > # Total_hitcount: 44 > #--------------------------------------- > > Is it possible to have something like that? > ------------------------------------------- > Total finds: 40 > Total hitcount: 44 > Total sequences: 50 > -------------------------------------------- Interesting question. It is more difficult than it seems. In the current output, "Total_sequences" is the number of times the report output has been called. Fuzznuc (and other programs) only call report output functions when they have something to report. Only the calling program (fuzznuc) knows how many sequences were read. However, the tail is written when the report file is closed, so we can simply pass the total number of input sequences to a version of ajReportClose, or add a function that sets a value for the report tail. We will add it to the next release. regards, Peter Rice From jison at ebi.ac.uk Tue Nov 4 15:34:02 2008 From: jison at ebi.ac.uk (Jon Ison) Date: Tue, 4 Nov 2008 15:34:02 -0000 (GMT) Subject: [EMBOSS] fuzznuc option report In-Reply-To: References: Message-ID: <56691.84.92.187.247.1225812842.squirrel@webmail.ebi.ac.uk> Hi Veronique The short answer is currently you can't. It would be easy to change the report and application code though (will discuss at next EMBOSS meeting). Cheers Jon > > Hi all, > > With fuzznuc how can I get in the report, the total sequences that there > are in my sequence list. > > At the end of the report, there is just the total of sequences found by > fuzznuc and the total hitcount, but I would like to known, how many > sequence was in my list at the begining. > In the following example my sequence list was 50 sequences. > > #--------------------------------------- > # Total_sequences: 40 > # Total_hitcount: 44 > #--------------------------------------- > > Is it possible to have something like that? > ------------------------------------------- > Total finds: 40 > Total hitcount: 44 > Total sequences: 50 > -------------------------------------------- > > Thanks and regards, > > Veronique > > ------------------------------------------------- > V?ronique MARTIN > INRA - Unit? Math?matique, Informatique et G?nome > 78352 Jouy-en Josas cedex > tel.: 01 34 65 29 74 > -------------------------------------------------_______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From db60 at st-andrews.ac.uk Tue Nov 4 16:00:26 2008 From: db60 at st-andrews.ac.uk (Daniel Barker) Date: Tue, 04 Nov 2008 16:00:26 +0000 Subject: [EMBOSS] fuzznuc option report In-Reply-To: <56691.84.92.187.247.1225812842.squirrel@webmail.ebi.ac.uk> References: <56691.84.92.187.247.1225812842.squirrel@webmail.ebi.ac.uk> Message-ID: <4910719A.4050003@st-andrews.ac.uk> >> With fuzznuc how can I get in the report, the total sequences >> that there are in my sequence list. If your sequences are in Fasta format, it's not too difficult to count sequences as separate step, prior to running the program, e.g. on Linux or OS X: grep -c '>' seqfile.fa Remember the single quotes, or else it won't work and even worse, you'll delete all sequences in the sequence file! Best wishes, Daniel -- Daniel Barker http://bio.st-andrews.ac.uk/staff/db60.htm The University of St Andrews is a charity registered in Scotland : No SC013532 From Perdeep.Mehta at STJUDE.ORG Tue Nov 4 17:08:03 2008 From: Perdeep.Mehta at STJUDE.ORG (Mehta, Perdeep) Date: Tue, 4 Nov 2008 11:08:03 -0600 Subject: [EMBOSS] extracting sequence from a pdb file In-Reply-To: References: Message-ID: <6EAE916704479E4BB6AB5A133BA224F70247E53D69@SJMEMXMBS11.stjude.sjcrh.local> Hi, Does anyone know if there is a program in EMBOSS that can extract protein sequence from a pdb format file? thanks, perdeep Perdeep K. Mehta, PhD Research Informatics, Information Sciences Division St. Jude Children's Research Hospital 262 Danny Thomas Place Memphis, TN 38105-2794 Tel: 901-495 3774 http://www.hatwellcenter.org/ From pmr at ebi.ac.uk Tue Nov 4 18:03:31 2008 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 04 Nov 2008 18:03:31 +0000 Subject: [EMBOSS] extracting sequence from a pdb file In-Reply-To: <6EAE916704479E4BB6AB5A133BA224F70247E53D69@SJMEMXMBS11.stjude.sjcrh.local> References: <6EAE916704479E4BB6AB5A133BA224F70247E53D69@SJMEMXMBS11.stjude.sjcrh.local> Message-ID: <49108E73.5030500@ebi.ac.uk> Mehta, Perdeep wrote: > Hi, > > Does anyone know if there is a program in EMBOSS that can extract protein sequence from a pdb format file? It depends on the pdb file format. There is a "pdb" sequence format that reads from the ATOM records, but fails on some pdb entries. There is also a "pdbseq" sequence format (-sf pdbseq on the command line) that reads the SEQRES records. If you find a PDB file that fails to read, please let us know. I just tested on an old 2ins entry file and it found zero sequences and failed (it was designed for a cleaned up PDB format). regards, Peter Rice From Perdeep.Mehta at STJUDE.ORG Tue Nov 4 20:42:40 2008 From: Perdeep.Mehta at STJUDE.ORG (Mehta, Perdeep) Date: Tue, 4 Nov 2008 14:42:40 -0600 Subject: [EMBOSS] extracting sequence from a pdb file In-Reply-To: <49108E73.5030500@ebi.ac.uk> References: <6EAE916704479E4BB6AB5A133BA224F70247E53D69@SJMEMXMBS11.stjude.sjcrh.local> <49108E73.5030500@ebi.ac.uk> Message-ID: <6EAE916704479E4BB6AB5A133BA224F70247E53D6A@SJMEMXMBS11.stjude.sjcrh.local> Thanks Peter. The file is standard ATOM record straight from PDB. I will check on that. Best regards, perdeep -----Original Message----- From: Peter Rice [mailto:pmr at ebi.ac.uk] Sent: Tuesday, November 04, 2008 12:04 PM To: emboss at emboss.open-bio.org Cc: Mehta, Perdeep Subject: Re: [EMBOSS] extracting sequence from a pdb file Mehta, Perdeep wrote: > Hi, > > Does anyone know if there is a program in EMBOSS that can extract protein sequence from a pdb format file? It depends on the pdb file format. There is a "pdb" sequence format that reads from the ATOM records, but fails on some pdb entries. There is also a "pdbseq" sequence format (-sf pdbseq on the command line) that reads the SEQRES records. If you find a PDB file that fails to read, please let us know. I just tested on an old 2ins entry file and it found zero sequences and failed (it was designed for a cleaned up PDB format). regards, Peter Rice From jison at ebi.ac.uk Wed Nov 5 12:24:28 2008 From: jison at ebi.ac.uk (Jon Ison) Date: Wed, 5 Nov 2008 12:24:28 -0000 (GMT) Subject: [EMBOSS] extracting sequence from a pdb file In-Reply-To: <6EAE916704479E4BB6AB5A133BA224F70247E53D69@SJMEMXMBS11.stjude.sjcrh.l ocal> References: <6EAE916704479E4BB6AB5A133BA224F70247E53D69@SJMEMXMBS11.stjude.sjcrh.local> Message-ID: <47987.84.92.187.247.1225887868.squirrel@webmail.ebi.ac.uk> Hi Perdeep You can use the program pdbparse from the "structure" EMBASSY package: http://emboss.sourceforge.net/apps/cvs/embassy/structure/ It will read ATOM / SEQRES records and write the true (corrected) molecular sequence (which is not an easy task!) to a file in a "clean" (easy to parse) format, which other EMBASSY packages can then make use of. There are various options for controlling how it handles e.g. missing atoms, mismatches, non-amino acid groups etc. in the original file. It's been a long while since I tested the program on the whole of PDB though so there are probably files it will fail for. If you need to extract the sequence into any specified sequence format then we could write a program for that (or something else) for the next release. Let me know. Cheers Jon > Hi, > > Does anyone know if there is a program in EMBOSS that can extract protein sequence from a pdb format file? > > thanks, > perdeep > > Perdeep K. Mehta, PhD > Research Informatics, Information Sciences Division > St. Jude Children's Research Hospital > 262 Danny Thomas Place > Memphis, TN 38105-2794 > Tel: 901-495 3774 > http://www.hatwellcenter.org/ > > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From mahvash.khalid at gmail.com Mon Nov 10 08:36:08 2008 From: mahvash.khalid at gmail.com (Mahvash Khalid) Date: Mon, 10 Nov 2008 13:36:08 +0500 Subject: [EMBOSS] (no subject) Message-ID: <67c424ae0811100036k40691baal500288fd0f7ac64e@mail.gmail.com> hiii.. iam a bioinformatics student and workin in linux .. my project is on coxepression of genes in humans ... but i dont know much abt java.. as java is the language which linux supports and not csharp.. i wanted to compare the start of mrna and coding regions to check the presence or absence of TSS ... if anyone can help i will be really grateful.. thanks mahvash From uludag at ebi.ac.uk Wed Nov 12 16:38:56 2008 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Wed, 12 Nov 2008 16:38:56 +0000 Subject: [EMBOSS] (no subject) In-Reply-To: <67c424ae0811100036k40691baal500288fd0f7ac64e@mail.gmail.com> References: <67c424ae0811100036k40691baal500288fd0f7ac64e@mail.gmail.com> Message-ID: <1226507936.21078.110.camel@emboss2.ebi.ac.uk> Hi Mahvash, > iam a bioinformatics student and workin in linux .. my project is on > coxepression of genes in humans ... but i dont know much abt java.. as java > is the language which linux supports and not csharp.. > i wanted to compare the start of mrna and coding regions to check the > presence or absence of TSS ... I talked to a colleague from the EBI RNA genomics group about your question. Harpreet told me you can do these comparisons using the Ensembl web site. I now forward your message to Harpreet. (If she can't post her answer to the emboss list, as she is not a member on the list, I will try posting on her behalf) Regards, Mahmut > if anyone can help i will be really grateful.. > thanks > mahvash From uludag at ebi.ac.uk Wed Nov 12 17:22:28 2008 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Wed, 12 Nov 2008 17:22:28 +0000 Subject: [EMBOSS] (no subject) In-Reply-To: <0A718E3F-2293-4567-B1AB-8C37211D4545@ebi.ac.uk> References: <67c424ae0811100036k40691baal500288fd0f7ac64e@mail.gmail.com> <1226507936.21078.110.camel@emboss2.ebi.ac.uk> <0A718E3F-2293-4567-B1AB-8C37211D4545@ebi.ac.uk> Message-ID: <1226510548.21078.138.camel@emboss2.ebi.ac.uk> If anyone else on the list is also interested to know how to get TSS information using Ensembl I forward Harpreet's message below. Harpreet told me "Eponine regions" feature should be used to get TSS information for Humans. Regards, Mahmut On Wed, 2008-11-12 at 16:46 +0000, Harpreet Saini wrote: > Hi Mahvash, > > I have used Ensembl web site many times to get the information about > the transcription start sites (TSS). You can get the TSS from the > features link in the Ensembl genome browser for your organism of > interest. > The other thing is that you can also easily obtain the start/end of > mRNA and coding regions from the Ensembl database using the Perl API. > If you have not used Ensembl or perl API before, then the ensembl web > site have very nice tutorials for beginners. > > Hope this will help you. > > Regards > Harpreet > > On 12 Nov 2008, at 16:38, Mahmut Uludag wrote: > > > Hi Mahvash, > > > >> iam a bioinformatics student and workin in linux .. my project is on > >> coxepression of genes in humans ... but i dont know much abt java.. > >> as java > >> is the language which linux supports and not csharp.. > >> i wanted to compare the start of mrna and coding regions to check the > >> presence or absence of TSS ... > > > > I talked to a colleague from the EBI RNA genomics group about your > > question. Harpreet told me you can do these comparisons using the > > Ensembl web site. I now forward your message to Harpreet. (If she > > can't > > post her answer to the emboss list, as she is not a member on the > > list, > > I will try posting on her behalf) > > > > Regards, > > Mahmut > > > >> if anyone can help i will be really grateful.. > >> thanks > >> mahvash > > > > Harpreet Kaur Saini > Enright Group > EMBL-European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD > Tel: +44-(0) 1223-492676 > > > > From db60 at st-andrews.ac.uk Wed Nov 12 17:55:45 2008 From: db60 at st-andrews.ac.uk (Daniel Barker) Date: Wed, 12 Nov 2008 17:55:45 +0000 Subject: [EMBOSS] (no subject) In-Reply-To: <1226510548.21078.138.camel@emboss2.ebi.ac.uk> References: <67c424ae0811100036k40691baal500288fd0f7ac64e@mail.gmail.com> <1226507936.21078.110.camel@emboss2.ebi.ac.uk> <0A718E3F-2293-4567-B1AB-8C37211D4545@ebi.ac.uk> <1226510548.21078.138.camel@emboss2.ebi.ac.uk> Message-ID: <491B18A1.7060000@st-andrews.ac.uk> Dear Mahmut, The Eponine regions would be TSS predicted by the Eponine program. This is different from the Ensembl Perl API approach Harpreet mentioned (e.g. use the API to get each Ensembl mRNA and see if its predicted start codon is at the beginning or not). It's fair to say both approaches will get you predictions, but different ones, due to different methodology used to generate the predictions. Best wishes, Daniel. Mahmut Uludag wrote: > If anyone else on the list is also interested to know how to get TSS > information using Ensembl I forward Harpreet's message below. Harpreet > told me "Eponine regions" feature should be used to get TSS information > for Humans. > > Regards, > Mahmut > > > On Wed, 2008-11-12 at 16:46 +0000, Harpreet Saini wrote: >> Hi Mahvash, >> >> I have used Ensembl web site many times to get the information about >> the transcription start sites (TSS). You can get the TSS from the >> features link in the Ensembl genome browser for your organism of >> interest. >> The other thing is that you can also easily obtain the start/end of >> mRNA and coding regions from the Ensembl database using the Perl API. >> If you have not used Ensembl or perl API before, then the ensembl web >> site have very nice tutorials for beginners. >> >> Hope this will help you. >> >> Regards >> Harpreet >> >> On 12 Nov 2008, at 16:38, Mahmut Uludag wrote: >> >>> Hi Mahvash, >>> >>>> iam a bioinformatics student and workin in linux .. my project is on >>>> coxepression of genes in humans ... but i dont know much abt java.. >>>> as java >>>> is the language which linux supports and not csharp.. >>>> i wanted to compare the start of mrna and coding regions to check the >>>> presence or absence of TSS ... >>> I talked to a colleague from the EBI RNA genomics group about your >>> question. Harpreet told me you can do these comparisons using the >>> Ensembl web site. I now forward your message to Harpreet. (If she >>> can't >>> post her answer to the emboss list, as she is not a member on the >>> list, >>> I will try posting on her behalf) >>> >>> Regards, >>> Mahmut >>> >>>> if anyone can help i will be really grateful.. >>>> thanks >>>> mahvash >> Harpreet Kaur Saini >> Enright Group >> EMBL-European Bioinformatics Institute >> Wellcome Trust Genome Campus >> Hinxton, Cambridge >> CB10 1SD >> Tel: +44-(0) 1223-492676 >> >> >> >> > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss -- Daniel Barker http://bio.st-andrews.ac.uk/staff/db60.htm The University of St Andrews is a charity registered in Scotland : No SC013532 From sylvain.foisy at diploide.net Mon Nov 24 21:20:13 2008 From: sylvain.foisy at diploide.net (Sylvain Foisy) Date: Mon, 24 Nov 2008 16:20:13 -0500 Subject: [EMBOSS] Compiling EMBOSS: missing jni.h? Message-ID: Hi, I'am trying to build a bioinfo workstation with Xubuntu and of course, I am trying to compile the latest EMBOSS (5.0 is the latest version of the pre-built package). I just hit a snag... After invoking make, it compiles for a while and then crashes with this (sorry for the length): Making all in ajax make[1]: Entering directory `/opt/bioxubuntu/sources/EMBOSS-6.0.1/ajax' /bin/bash ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"6.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -DPLD_png=1 -I. -DAJAX_FIXED_ROOT=\"/opt/bioxubuntu/sources/EMBOSS-6.0.1/emboss\" -DPREFIX=\"/usr/local\" -I../plplot -DPOSIX_MALLOC_THRESHOLD=10 -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DLENDIAN -I/usr/lib/jvm/java-6-openjdk/jre -DHAVE_JAVA -I/usr/lib/jvm/java-6-openjdk -DNO_AUTH -O2 -MT ajacd.lo -MD -MP -MF .deps/ajacd.Tpo -c -o ajacd.lo ajacd.c mkdir .libs gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"6.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -DPLD_png=1 -I. -DAJAX_FIXED_ROOT=\"/opt/bioxubuntu/sources/EMBOSS-6.0.1/emboss\" -DPREFIX=\"/usr/local\" -I../plplot -DPOSIX_MALLOC_THRESHOLD=10 -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DLENDIAN -I/usr/lib/jvm/java-6-openjdk/jre -DHAVE_JAVA -I/usr/lib/jvm/java-6-openjdk -DNO_AUTH -O2 -MT ajacd.lo -MD -MP -MF .deps/ajacd.Tpo -c ajacd.c -fPIC -DPIC -o .libs/ajacd.o In file included from ajax.h:77, from ajacd.c:41: ajjava.h:13:17: error: jni.h: No such file or directory In file included from ajax.h:77, from ajacd.c:41: ajjava.h:33: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:35: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:38: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:41: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jint' ajjava.h:43: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jint' ajjava.h:45: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jint' ajjava.h:47: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jint' ajjava.h:50: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jint' ajjava.h:52: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jint' ajjava.h:54: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jint' ajjava.h:56: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jint' ajjava.h:60: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:67: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:71: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:75: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:79: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:83: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:87: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:91: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:96: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:101: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:106: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jbyteArray' ajjava.h:111: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:116: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' ajjava.h:121: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'jboolean' make[1]: *** [ajacd.lo] Error 1 make[1]: Leaving directory `/opt/bioxubuntu/sources/EMBOSS-6.0.1/ajax' make: *** [all-recursive] Error 1 Can anyone point me toward a solution? I have openjdk-6-jdk installed via apt-get but it seems that I am missing something... Best regards Sylvain ================================================================== Sylvain Foisy, Ph. D. Charg? de projet / Project Manager Bio-informatique Adresse postale: Laboratoire de genetique et medecine genomique de l'inflammation Institut de cardiologie de Montreal 5000 Belanger Montreal, Qc H1T 1C8 T: 514-376-3330 x.2299 | F: 514-593-2539 M: sylvain.foisy at inflammgen.org W: http://www.inflammgen.org ================================================================== From charles-listes-emboss at plessy.org Tue Nov 25 05:55:38 2008 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Tue, 25 Nov 2008 14:55:38 +0900 Subject: [EMBOSS] Compiling EMBOSS: missing jni.h? In-Reply-To: References: Message-ID: <20081125055538.GD8418@kunpuu.plessy.org> Le Mon, Nov 24, 2008 at 04:20:13PM -0500, Sylvain Foisy a ?crit : > Hi, > > I'am trying to build a bioinfo workstation with Xubuntu and of course, I am > trying to compile the latest EMBOSS (5.0 is the latest version of the > pre-built package). I just hit a snag... After invoking make, it compiles > for a while and then crashes with this (sorry for the length): Hello Sylvain, There is a Debian package ready for EMBOSS 6.0.1 in our experimental section. If you do not need jEMBOSS (that is not yet supported by our packages), you can either try to install directly the binary packages, or to compile them on your system: - Get the build tools: sudo aptitude install devscripts build-essential - Get the source package: dget -x http://ftp.de.debian.org/debian/pool/main/e/emboss/emboss_6.0.1-2.dsc - Get the build dependancies: cd emboss-6.0.1 ; sudo mk-build-deps -r -i - Make the binary packages: debuild - Install them: cd .. ; sudo dpkg -i emboss_6.0.1-2_*.deb emboss-data_6.0.1-2_all.deb emboss-doc_6.0.1-2_all.deb emboss-lib_6.0.1-2_*.deb libajax6_6.0.1-2_*.deb libnucleus6_6.0.1-2_*.deb Another way is to contact the Ubuntu MOTUs and ask them to synchronise with the Debian experimental package. The only reason why it is there is that Debian is frozen now, preparing its release. It will be part of the main distribution later (and the embassy packages will be rebuilt against it). > Can anyone point me toward a solution? I have openjdk-6-jdk installed via > apt-get but it seems that I am missing something... Have you passed the following arguments to your configure script: --with-java=/usr/lib/jvm/java-6-openjdk/include --with-javaos=/usr/lib/jvm/java-6-openjdk/include/linux Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From sylvain.foisy at diploide.net Tue Nov 25 15:22:52 2008 From: sylvain.foisy at diploide.net (Sylvain Foisy) Date: Tue, 25 Nov 2008 10:22:52 -0500 Subject: [EMBOSS] Compiling EMBOSS: missing jni.h? Message-ID: Hi, Thanks for the inputs on the paths toward java/javaos; make/make install now worked...kind of. I need the Jemboss interface to facilitate my students' interactions with EMBOSS, this is why I want to compile myself. Now the "kind of" part: I hit a "libnucleus.so.6 not found" and it seems to be related to the fact that libeplplot.so.3 is not found. I know that I have the libplplot9/libplplot-dev packages installed. Any pointers? Could I use your experimental package for emboss-libs to fix this? Thanks for the help Sylvain ================================================================== Sylvain Foisy, Ph. D. Charg? de projet / Project Manager Bio-informatique Adresse postale: Laboratoire de genetique et medecine genomique de l'inflammation Institut de cardiologie de Montreal 5000 Belanger Montreal, Qc H1T 1C8 T: 514-376-3330 x.2299 | F: 514-593-2539 M: sylvain.foisy at inflammgen.org W: http://www.inflammgen.org ================================================================== From charles-listes-emboss at plessy.org Wed Nov 26 13:17:27 2008 From: charles-listes-emboss at plessy.org (charles-listes-emboss at plessy.org) Date: Wed, 26 Nov 2008 22:17:27 +0900 Subject: [EMBOSS] Compiling EMBOSS: missing jni.h? In-Reply-To: References: Message-ID: <20081126131727.GJ21391@kunpuu.plessy.org> Le Tue, Nov 25, 2008 at 10:22:52AM -0500, Sylvain Foisy a ?crit : > > Thanks for the inputs on the paths toward java/javaos; make/make install now > worked...kind of. I need the Jemboss interface to facilitate my students' > interactions with EMBOSS, this is why I want to compile myself. > > Now the "kind of" part: I hit a "libnucleus.so.6 not found" and it seems to > be related to the fact that libeplplot.so.3 is not found. I know that I have > the libplplot9/libplplot-dev packages installed. Any pointers? Could I use > your experimental package for emboss-libs to fix this? Hi Sylvain, EMBOSS uses a fork of libplplot, that was named libeplplot to allow both libraries to be installed on the same system. (By the way, is the fork still needed?) What seems to happen on your system is that it does not find the nucleus and eplplot libraries. Although it is not really recommended to mix local and packaged installs, the packages libajax6, libnucleus6 and emboss-lib may provide you what you need. I have started to implement support for jEMBOSS in the Debian packages, but it will take time before it reaches Debian archives. What you can do if you would like to try it is to unpack the emboss sources, and within them type "debcheckout emboss". Then you can use the protocol I gave you before, with mk-build-deps if still needed, and then debuild. On my amd64 system, I just checked that something would appear whan running runJemboss, but did not verify further that it functions correctly. Lastly, if all you need is an interface, you can try the emboss-explorer package, that provides a web frontend to EMBOSS. Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From golharam at umdnj.edu Wed Nov 26 14:50:05 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Wed, 26 Nov 2008 09:50:05 -0500 Subject: [EMBOSS] Compiling EMBOSS: missing jni.h? In-Reply-To: <20081126131727.GJ21391@kunpuu.plessy.org> References: <20081126131727.GJ21391@kunpuu.plessy.org> Message-ID: <492D621D.6050104@umdnj.edu> You can obtain EMBOSS RPMs from http://informatics.umdnj.edu/BioRPMs They compile cleanly and document dependencies. charles-listes-emboss at plessy.org wrote: > Le Tue, Nov 25, 2008 at 10:22:52AM -0500, Sylvain Foisy a ?crit : >> Thanks for the inputs on the paths toward java/javaos; make/make install now >> worked...kind of. I need the Jemboss interface to facilitate my students' >> interactions with EMBOSS, this is why I want to compile myself. >> >> Now the "kind of" part: I hit a "libnucleus.so.6 not found" and it seems to >> be related to the fact that libeplplot.so.3 is not found. I know that I have >> the libplplot9/libplplot-dev packages installed. Any pointers? Could I use >> your experimental package for emboss-libs to fix this? > > Hi Sylvain, > > EMBOSS uses a fork of libplplot, that was named libeplplot to allow both > libraries to be installed on the same system. (By the way, is the fork still > needed?) What seems to happen on your system is that it does not find the > nucleus and eplplot libraries. Although it is not really recommended to mix > local and packaged installs, the packages libajax6, libnucleus6 and emboss-lib > may provide you what you need. > > I have started to implement support for jEMBOSS in the Debian packages, but it > will take time before it reaches Debian archives. What you can do if you would > like to try it is to unpack the emboss sources, and within them type > "debcheckout emboss". Then you can use the protocol I gave you before, with > mk-build-deps if still needed, and then debuild. On my amd64 system, I just > checked that something would appear whan running runJemboss, but did not verify > further that it functions correctly. > > Lastly, if all you need is an interface, you can try the emboss-explorer > package, that provides a web frontend to EMBOSS. > > Have a nice day, > -------------- next part -------------- A non-text attachment was scrubbed... Name: golharam.vcf Type: text/x-vcard Size: 439 bytes Desc: not available URL: