From philipp.pagel at cmp.yale.edu Sat Dec 2 17:39:33 2000 From: philipp.pagel at cmp.yale.edu (Philipp Pagel) Date: Sat, 02 Dec 2000 17:39:33 -0500 Subject: Hello - anybody out there? Message-ID: <3A297A25.C3BE0289@cmp.yale.edu> Hi! I apologise for this OT posting but I was really wondering if this is a problem on my side, or if there IS no traffic on this list... Anyway: I just downloaded EMBOSS 1.8 on my SUSE LINUX box and started to play with it. I really liked what I have seen so far. Only the lack of any GUI wrapper for small and dirty jobs is a pitty. OK - www interfaces - but I really don't like them. That makes me wonder if anybody knows about an ongoing project for a GUI for EMBOSS implemented in C or whatever. I am not a big coding guru, but I might be interested in participating if I can find a little time... cu Philipp -- Dr. Philipp Pagel Cellular and Molecular Physiology phone: (203) 785-6835 SHM BE-30 Yale University 333 Cedar ST New Haven, CT 06520 From milius at bscl.msi.umn.edu Fri Dec 1 18:14:45 2000 From: milius at bscl.msi.umn.edu (Robert Milius) Date: Fri, 1 Dec 2000 15:14:45 -0800 Subject: Hello - anybody out there? In-Reply-To: <3A297A25.C3BE0289@cmp.yale.edu> Message-ID: Hello, It looks like there are several efforts underway: http://www.uk.embnet.org/Software/EMBOSS//Doc/interfaces.html for example, coilmate looks like a non-www gui interface being developed though I don't know how far along they are. -bob On Sat, 2 Dec 2000, Philipp Pagel wrote: > Hi! > > I apologise for this OT posting but I was really wondering if this is a > problem on my side, or if there IS no traffic on this list... > > Anyway: I just downloaded EMBOSS 1.8 on my SUSE LINUX box and started to > play with it. I really liked what I have seen so far. > Only the lack of any GUI wrapper for small and dirty jobs is a pitty. > OK - www interfaces - but I really don't like them. > > That makes me wonder if anybody knows about an ongoing project for a > GUI for EMBOSS implemented in C or whatever. I am not a big coding guru, > but I might be interested in participating if I can find a little > time... > > cu > Philipp > > -- > Dr. Philipp Pagel > Cellular and Molecular Physiology phone: (203) 785-6835 > SHM BE-30 > Yale University > 333 Cedar ST > New Haven, CT 06520 > > Robert P. Milius, Ph.D. 612-626-2771 (office) Basic Sciences Computing Laboratory 612-625-4433 (fax) University of Minnesota Supercomputing Institute milius at msi.umn.edu for Digital Simulation and Advanced Computation From ableasby at hgmp.mrc.ac.uk Fri Dec 1 19:58:43 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Sat, 2 Dec 2000 00:58:43 GMT Subject: Hello - anybody out there? Message-ID: <200012020058.AAA10460@tin.hgmp.mrc.ac.uk> There is an interface being created by the Staden group which has been delayed by maternity leave. Another GUI is very near completion at DKFZ. Alan From LL at earthling.net Mon Dec 4 00:32:59 2000 From: LL at earthling.net (Long LIANG) Date: Mon, 04 Dec 2000 13:32:59 +0800 Subject: MEME Message-ID: <3A2B2C8B.6030602@earthling.net> Hi, I got such messages when compiled in RedHat 7.0 . could someone help me? ...... make[2]: Entering directory `/usr/local/EMBOSS/EMBOSS-1.8.0/embassy/MEME-2.3.1/src' /bin/sh ../libtool --mode=link gcc -O -o meme meme.o libmeme.la ../../../ajax/libajax.la -lncurses -lcurses -lm gcc -O -o .libs/meme meme.o .libs/libmeme.so -lncurses -lcurses -lm ../../../ajax/.libs/libajax.so -lm -lz -lgd -lpng -lncurses -lcurses -lm -Wl,--rpath -Wl,/usr/local/EMBOSS/lib .libs/libmeme.so: undefined reference to `diagram' .libs/libmeme.so: undefined reference to `space' .libs/libmeme.so: undefined reference to `norder' .libs/libmeme.so: undefined reference to `dptr' .libs/libmeme.so: undefined reference to `order' collect2: ld returned 1 exit status make[2]: *** [meme] Error 1 make[2]: Leaving directory `/usr/local/EMBOSS/EMBOSS-1.8.0/embassy/MEME-2.3.1/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/usr/local/EMBOSS/EMBOSS-1.8.0/embassy/MEME-2.3.1/src' make: *** [all-recursive] Error 1 From bauer at genprofile.com Mon Dec 4 02:55:17 2000 From: bauer at genprofile.com (David Bauer) Date: Mon, 04 Dec 2000 08:55:17 +0100 Subject: MEME References: <3A2B2C8B.6030602@earthling.net> Message-ID: <3A2B4DE5.BF66C9D9@genprofile.com> Hi, I'm getting the same errors when building MEME on FreeBSD, and a new problem with EMBOSS-1.8.0 itself: Configure writes wrong LDFLAGS in the ajax/Makefile. What I get there is "-no-undefined" which results in failing to find the libs. After changing this to -L/usr/local/lib gcc is happy again. David. Long LIANG wrote: > > Hi, > > I got such messages when compiled in RedHat 7.0 . could someone help me? > > ...... > make[2]: Entering directory > `/usr/local/EMBOSS/EMBOSS-1.8.0/embassy/MEME-2.3.1/src' > /bin/sh ../libtool --mode=link gcc -O -o meme meme.o libmeme.la > ../../../ajax/libajax.la -lncurses -lcurses -lm > gcc -O -o .libs/meme meme.o .libs/libmeme.so -lncurses -lcurses -lm > ../../../ajax/.libs/libajax.so -lm -lz -lgd -lpng -lncurses -lcurses -lm > -Wl,--rpath -Wl,/usr/local/EMBOSS/lib > .libs/libmeme.so: undefined reference to `diagram' > .libs/libmeme.so: undefined reference to `space' > .libs/libmeme.so: undefined reference to `norder' > .libs/libmeme.so: undefined reference to `dptr' > .libs/libmeme.so: undefined reference to `order' > collect2: ld returned 1 exit status > make[2]: *** [meme] Error 1 > make[2]: Leaving directory > `/usr/local/EMBOSS/EMBOSS-1.8.0/embassy/MEME-2.3.1/src' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory > `/usr/local/EMBOSS/EMBOSS-1.8.0/embassy/MEME-2.3.1/src' > make: *** [all-recursive] Error 1 -- Dr. David Bauer GenProfile AG, Max-Delbrueck-Center, Erwin-Negelein-Haus Robert-Roessle-Str. 10, D-13125 Berlin, Germany bauer at genprofile.com, Tel:49-30-94892165, FAX:49-30-94892151 From ableasby at hgmp.mrc.ac.uk Mon Dec 4 06:35:45 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Mon, 4 Dec 2000 11:35:45 GMT Subject: MEME Message-ID: <200012041135.LAA24395@tin.hgmp.mrc.ac.uk> I've put in a fix for this. There is a new MEME tarball on the ftp server under the same name as before. I'm intrigued about the separate LDFLAGS in AJAX for FreeBSD. As far as I know the ajax configure hasn't changed in many months. If you can get back to me with more complete error msgs I can take a look. btw: I am on holiday so apologies if the response time to queries is slow. Alan From johann at egenetics.com Mon Dec 4 07:55:47 2000 From: johann at egenetics.com (Johann Visagie) Date: Mon, 4 Dec 2000 14:55:47 +0200 Subject: MEME In-Reply-To: <3A2B4DE5.BF66C9D9@genprofile.com>; from bauer@genprofile.com on Mon, Dec 04, 2000 at 08:55:17AM +0100 References: <3A2B2C8B.6030602@earthling.net> <3A2B4DE5.BF66C9D9@genprofile.com> Message-ID: <20001204145547.E9796@fling.sanbi.ac.za> David Bauer on 2000-12-04 (Mon) at 08:55:17 +0100: > > I'm getting the same errors when building MEME on FreeBSD, and a new > problem with EMBOSS-1.8.0 itself: > Configure writes wrong LDFLAGS in the ajax/Makefile. What I get there is > "-no-undefined" which results in failing to find the libs. > After changing this to -L/usr/local/lib gcc is happy again. Which version of FreeBSD are you building on? I'm constantly building EMBOSS on FreeBSD - several builds are usually required every time I change anything to the FreeBSD EMBOSS port - and I've not seen the build breaking, ever. (Though I'm doing another build now to be sure.) I do all my development and testing on 5.0-CURRENT these days, though. BTW, the FreeBSD EMBOSS port now includes the EMBASSY applications MSE, PHYLIP and TOPO. Upon installation the user is given an ncurses-based full-screen menu in order to decide which of them to install. I'll add MEME to the port soon as well, and EMNU when it's available. -- Johann From coss at cnb.uam.es Tue Dec 5 06:03:13 2000 From: coss at cnb.uam.es (=?ISO-8859-1?Q?Carlos_Oscar_S=E1nchez_Sorzano?=) Date: Tue, 5 Dec 2000 12:03:13 +0100 Subject: Hello - anybody out there? In-Reply-To: Message-ID: Hello, On Fri, 1 Dec 2000, Robert Milius wrote: > Hello, > > It looks like there are several efforts underway: > > http://www.uk.embnet.org/Software/EMBOSS//Doc/interfaces.html > > for example, coilmate looks like a non-www gui interface > being developed though I don't know how far along they are. > > -bob The colimate interface is going on, there are still several things that must be worked out inside Colimate and then the translation of the ACD files should not be a big problem. I hope that it can be ready in 2 or 3 months. Carlos Oscar. > On Sat, 2 Dec 2000, Philipp Pagel wrote: > > > Hi! > > > > I apologise for this OT posting but I was really wondering if this is a > > problem on my side, or if there IS no traffic on this list... > > > > Anyway: I just downloaded EMBOSS 1.8 on my SUSE LINUX box and started to > > play with it. I really liked what I have seen so far. > > Only the lack of any GUI wrapper for small and dirty jobs is a pitty. > > OK - www interfaces - but I really don't like them. > > > > That makes me wonder if anybody knows about an ongoing project for a > > GUI for EMBOSS implemented in C or whatever. I am not a big coding guru, > > but I might be interested in participating if I can find a little > > time... > > > > cu > > Philipp > > > > -- > > Dr. Philipp Pagel > > Cellular and Molecular Physiology phone: (203) 785-6835 > > SHM BE-30 > > Yale University > > 333 Cedar ST > > New Haven, CT 06520 > > > > > > Robert P. Milius, Ph.D. 612-626-2771 (office) > Basic Sciences Computing Laboratory 612-625-4433 (fax) > University of Minnesota Supercomputing Institute milius at msi.umn.edu > for Digital Simulation and Advanced Computation > > ----------------------------------------------------------------------------- Carlos Oscar S?nchez Sorzano e-mail: coss at cnb.uam.es Unidad de Bioinform?tica http://biocomp.cnb.uam.es Centro Nacional de Biotecnolog?a (CSIC) Campus Universidad Autonoma (Cantoblanco) Tlf: 34-91-585 4683 28049 MADRID (SPAIN) Fax: 34-91-585 4506 ----------------------------------------------------------------------------- From starksb at ebi.ac.uk Tue Dec 5 12:01:27 2000 From: starksb at ebi.ac.uk (David Starks-Browning) Date: Tue, 5 Dec 2000 17:01:27 +0000 Subject: any success with gcc-2.95.2 on Digital Unix? Message-ID: <1188-Tue05Dec2000170127+0000-starksb@ebi.ac.uk> Greeting EMBOSS users, Has anyone successfully built EMBOSS with gcc-2.95.2 on Digital Unix? When I try it, I get syntax errors in ajax/ajfmt.c wherever var_arg is used. It compiles fine with gcc-2.95.2 on other platforms (including IRIX and Linux), so it's probably not a problem with EMBOSS, except possibly via autoconf. Also, the Digital cc build is fine. This is with EMBOSS-1.8.0, though I have always had this problem (though I do not check it regularly). Before I investigate further (it's probably a gcc bug), I thought I would ask if others have had the same experience, in case it's just a problem with my gcc installation. Thanks for your help. Regards, David ------------------------------------------------------------------- David Starks-Browning | starksb at ebi.ac.uk EMBL Outstation -- | The European Bioinformatics Institute | Wellcome Trust Genome Campus | tel: +44 (1223) 494 616 Hinxton, Cambridge, CB10 1SD, UK | fax: +44 (1223) 494 468 ------------------------------------------------------------------- From roels at mpi.com Thu Dec 14 16:16:09 2000 From: roels at mpi.com (Steve Roels) Date: Thu, 14 Dec 2000 16:16:09 -0500 Subject: use of full genbank style ids Message-ID: <3A393899.9D2656EF@mpi.com> Hello, Anyone know if there is a way to force the use of full genbank-style sequence identifiers in output files? for example: >gi|12345|gb|AC00123.4|HUDDR GGCGCGCCG... The id used is either "gi" (if fasta format is specified - or no format is specified) or "gb|AC00123.4|HUDDR" (if ncbi format is specified). In short (and to be more general), what I want is to have everything up to the first white-space (i.e. including vertical bars,colons,etc) to be treated as the id. Thanks, -Steve -- ***************************************************************** Steve Roels, Ph.D. Scientist - Computational Biology Phone: (617) 761-6820 Millennium Pharmaceuticals, Inc. FAX: (617) 577-3568 640 Memorial Drive Email: roels at mpi.com Cambridge, MA 02139-4815 ***************************************************************** From Peter.Rice at uk.lionbioscience.com Fri Dec 15 04:50:48 2000 From: Peter.Rice at uk.lionbioscience.com (Peter Rice) Date: Fri, 15 Dec 2000 09:50:48 +0000 Subject: use of full genbank style ids References: <3A393899.9D2656EF@mpi.com> Message-ID: <3A39E978.46E7EBF6@lionbio.co.uk> Steve Roels wrote: > > Anyone know if there is a way to force the use of full genbank-style sequence identifiers > in output files? > > >gi|12345|gb|AC00123.4|HUDDR > GGCGCGCCG... > > The id used is either "gi" (if fasta format is specified - or no format is specified) or > "gb|AC00123.4|HUDDR" (if ncbi format is specified). > > In short (and to be more general), what I want is to have everything up to the first > white-space (i.e. including vertical bars,colons,etc) to be treated as the id. Possible - by defining a new format. Not a big code change. 'GenBank' is of course the 'wrong' name - as we use that for the CODATA format GENBANK files. This is really NCBI's blast version of the FASTA format. Any suggestions for a format name? You want to include the GI number in parsing, and also pick up the sequence version rather than just the accession number. One question would be - what would you like to use as a filename on output? Unix will not be happy with those '|' characters in a filename, so we would normally trim it back to the ID at the end. I guess the '|' could also break future extensions to the USA syntax if you plan to use these IDs in USAs. We already use '|' at the end to pipe application output (perl style). We could, in theory, use SRS syntax to offer alternative IDs or accession numbers. For example, SRS accepts swissprot-id:amic_ecoli|amic_pseae|amic_strpn and returns 3 entries. Any takers for this syntax in EMBOSS? -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From roels at mpi.com Fri Dec 15 10:07:44 2000 From: roels at mpi.com (Steve Roels) Date: Fri, 15 Dec 2000 10:07:44 -0500 Subject: use of full genbank style ids References: <3A393899.9D2656EF@mpi.com> <3A39E978.46E7EBF6@lionbio.co.uk> Message-ID: <3A3A33C0.BB28593A@mpi.com> Peter et al, Thanks for the quick reply. A few more comments follow. Peter Rice wrote: > > Steve Roels wrote: > > > > Anyone know if there is a way to force the use of full genbank-style sequence identifiers > > in output files? > > > > >gi|12345|gb|AC00123.4|HUDDR > > GGCGCGCCG... > > > > The id used is either "gi" (if fasta format is specified - or no format is specified) or > > "gb|AC00123.4|HUDDR" (if ncbi format is specified). > > > > In short (and to be more general), what I want is to have everything up to the first > > white-space (i.e. including vertical bars,colons,etc) to be treated as the id. > > Possible - by defining a new format. Not a big code change. > > 'GenBank' is of course the 'wrong' name - as we use that for the CODATA > format GENBANK files. This is really NCBI's blast version of the FASTA > format. Any suggestions for a format name? Yes - I should have been more specific. I meant NCBI's style for fasta header ids. Generally: databasetag|id(|possiblymorealiasesorids) and (to be more general still, the ":" equivalent) databasetag:id(:possiblymorealiasesorids) Note to that it could be treated as a two step process: (1) To handle ids most generally, have a format that grabs everything up to the first white space as an id, including delimiters like '|' and ":". You need not try to extract the elements of the id (gid,accession,version,locus for genbank fasta ids for example). Here you leave interpretation of the full id to the user - you just provide a way to pass ids intact from the input file to the output file. This would work for those ( hypothetically speaking :) ) that use the ">dbtag|id" or ">dbtag:id" structure for there own data. Even if I converted an id like "mydb|12345" to "mydb:12345" and specified fasta format, the dbtag is dropped in the output, rendering the id in the output potentially ambiguous. (2) If desired (I don't really need it), expand on #1 (as the "ncbi" format seem to try to do) so that, for example, "sp|P12345" would be recognized as swissprot entry with accession P12345, and "gi|12345|gb|AC00123.4|HUDDR" would be recognized as genbank entry with gid 12345, accession AC00123, version 4, and locus HUDDR. The parsed accessions,locus names,gids, etc could then be used in some contexts. But even here, I'd like the option of putting the full id (including database/source tag) in the output. > > You want to include the GI number in parsing, and also pick up the sequence > version rather than just the accession number. > > One question would be - what would you like to use as a filename on output? > Unix will not be happy with those '|' characters in a filename, so we > would normally trim it back to the ID at the end. I agree this is a problem with the use of "|" as a delimiter. In naming files, we've typically resorted to substituting another character (e.g. "_") for "|" to generate files like: gi_12345_gb_AC00123.4_HUDDR.output or more simply (since the aliases/alt_ids are not really needed): gi_12345.output The key is to have the full id in the output file, and a unique name for the output file. Using just 12345.output for the file, or "12345" in that output file, could be problematic if you have a sequence with id 12345 from more than one database/source. > > I guess the '|' could also break future extensions to the USA syntax if you > plan to use these IDs in USAs. We already use '|' at the end to pipe > application output (perl style). We could, in theory, use SRS syntax > to offer alternative IDs or accession numbers. For example, SRS accepts > swissprot-id:amic_ecoli|amic_pseae|amic_strpn and returns 3 entries. > Any takers for this syntax in EMBOSS? Obviously, I wouldn't want to wreak havoc with the large body of code already in place or envisioned. But if its a simple new format... Thanks again, -Steve > > -- > ------------------------------------------------ > Peter Rice, LION Bioscience Ltd, Cambridge, UK > peter.rice at uk.lionbioscience.com +44 1223 224723 -- ***************************************************************** Steve Roels, Ph.D. Scientist - Computational Biology Phone: (617) 761-6820 Millennium Pharmaceuticals, Inc. FAX: (617) 577-3568 640 Memorial Drive Email: roels at mpi.com Cambridge, MA 02139-4815 ***************************************************************** From philipp.pagel at cmp.yale.edu Sat Dec 2 22:39:33 2000 From: philipp.pagel at cmp.yale.edu (Philipp Pagel) Date: Sat, 02 Dec 2000 17:39:33 -0500 Subject: Hello - anybody out there? Message-ID: <3A297A25.C3BE0289@cmp.yale.edu> Hi! I apologise for this OT posting but I was really wondering if this is a problem on my side, or if there IS no traffic on this list... Anyway: I just downloaded EMBOSS 1.8 on my SUSE LINUX box and started to play with it. I really liked what I have seen so far. Only the lack of any GUI wrapper for small and dirty jobs is a pitty. OK - www interfaces - but I really don't like them. That makes me wonder if anybody knows about an ongoing project for a GUI for EMBOSS implemented in C or whatever. I am not a big coding guru, but I might be interested in participating if I can find a little time... cu Philipp -- Dr. Philipp Pagel Cellular and Molecular Physiology phone: (203) 785-6835 SHM BE-30 Yale University 333 Cedar ST New Haven, CT 06520 From milius at bscl.msi.umn.edu Fri Dec 1 23:14:45 2000 From: milius at bscl.msi.umn.edu (Robert Milius) Date: Fri, 1 Dec 2000 15:14:45 -0800 Subject: Hello - anybody out there? In-Reply-To: <3A297A25.C3BE0289@cmp.yale.edu> Message-ID: Hello, It looks like there are several efforts underway: http://www.uk.embnet.org/Software/EMBOSS//Doc/interfaces.html for example, coilmate looks like a non-www gui interface being developed though I don't know how far along they are. -bob On Sat, 2 Dec 2000, Philipp Pagel wrote: > Hi! > > I apologise for this OT posting but I was really wondering if this is a > problem on my side, or if there IS no traffic on this list... > > Anyway: I just downloaded EMBOSS 1.8 on my SUSE LINUX box and started to > play with it. I really liked what I have seen so far. > Only the lack of any GUI wrapper for small and dirty jobs is a pitty. > OK - www interfaces - but I really don't like them. > > That makes me wonder if anybody knows about an ongoing project for a > GUI for EMBOSS implemented in C or whatever. I am not a big coding guru, > but I might be interested in participating if I can find a little > time... > > cu > Philipp > > -- > Dr. Philipp Pagel > Cellular and Molecular Physiology phone: (203) 785-6835 > SHM BE-30 > Yale University > 333 Cedar ST > New Haven, CT 06520 > > Robert P. Milius, Ph.D. 612-626-2771 (office) Basic Sciences Computing Laboratory 612-625-4433 (fax) University of Minnesota Supercomputing Institute milius at msi.umn.edu for Digital Simulation and Advanced Computation From ableasby at hgmp.mrc.ac.uk Sat Dec 2 00:58:43 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Sat, 2 Dec 2000 00:58:43 GMT Subject: Hello - anybody out there? Message-ID: <200012020058.AAA10460@tin.hgmp.mrc.ac.uk> There is an interface being created by the Staden group which has been delayed by maternity leave. Another GUI is very near completion at DKFZ. Alan From LL at earthling.net Mon Dec 4 05:32:59 2000 From: LL at earthling.net (Long LIANG) Date: Mon, 04 Dec 2000 13:32:59 +0800 Subject: MEME Message-ID: <3A2B2C8B.6030602@earthling.net> Hi, I got such messages when compiled in RedHat 7.0 . could someone help me? ...... make[2]: Entering directory `/usr/local/EMBOSS/EMBOSS-1.8.0/embassy/MEME-2.3.1/src' /bin/sh ../libtool --mode=link gcc -O -o meme meme.o libmeme.la ../../../ajax/libajax.la -lncurses -lcurses -lm gcc -O -o .libs/meme meme.o .libs/libmeme.so -lncurses -lcurses -lm ../../../ajax/.libs/libajax.so -lm -lz -lgd -lpng -lncurses -lcurses -lm -Wl,--rpath -Wl,/usr/local/EMBOSS/lib .libs/libmeme.so: undefined reference to `diagram' .libs/libmeme.so: undefined reference to `space' .libs/libmeme.so: undefined reference to `norder' .libs/libmeme.so: undefined reference to `dptr' .libs/libmeme.so: undefined reference to `order' collect2: ld returned 1 exit status make[2]: *** [meme] Error 1 make[2]: Leaving directory `/usr/local/EMBOSS/EMBOSS-1.8.0/embassy/MEME-2.3.1/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/usr/local/EMBOSS/EMBOSS-1.8.0/embassy/MEME-2.3.1/src' make: *** [all-recursive] Error 1 From bauer at genprofile.com Mon Dec 4 07:55:17 2000 From: bauer at genprofile.com (David Bauer) Date: Mon, 04 Dec 2000 08:55:17 +0100 Subject: MEME References: <3A2B2C8B.6030602@earthling.net> Message-ID: <3A2B4DE5.BF66C9D9@genprofile.com> Hi, I'm getting the same errors when building MEME on FreeBSD, and a new problem with EMBOSS-1.8.0 itself: Configure writes wrong LDFLAGS in the ajax/Makefile. What I get there is "-no-undefined" which results in failing to find the libs. After changing this to -L/usr/local/lib gcc is happy again. David. Long LIANG wrote: > > Hi, > > I got such messages when compiled in RedHat 7.0 . could someone help me? > > ...... > make[2]: Entering directory > `/usr/local/EMBOSS/EMBOSS-1.8.0/embassy/MEME-2.3.1/src' > /bin/sh ../libtool --mode=link gcc -O -o meme meme.o libmeme.la > ../../../ajax/libajax.la -lncurses -lcurses -lm > gcc -O -o .libs/meme meme.o .libs/libmeme.so -lncurses -lcurses -lm > ../../../ajax/.libs/libajax.so -lm -lz -lgd -lpng -lncurses -lcurses -lm > -Wl,--rpath -Wl,/usr/local/EMBOSS/lib > .libs/libmeme.so: undefined reference to `diagram' > .libs/libmeme.so: undefined reference to `space' > .libs/libmeme.so: undefined reference to `norder' > .libs/libmeme.so: undefined reference to `dptr' > .libs/libmeme.so: undefined reference to `order' > collect2: ld returned 1 exit status > make[2]: *** [meme] Error 1 > make[2]: Leaving directory > `/usr/local/EMBOSS/EMBOSS-1.8.0/embassy/MEME-2.3.1/src' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory > `/usr/local/EMBOSS/EMBOSS-1.8.0/embassy/MEME-2.3.1/src' > make: *** [all-recursive] Error 1 -- Dr. David Bauer GenProfile AG, Max-Delbrueck-Center, Erwin-Negelein-Haus Robert-Roessle-Str. 10, D-13125 Berlin, Germany bauer at genprofile.com, Tel:49-30-94892165, FAX:49-30-94892151 From ableasby at hgmp.mrc.ac.uk Mon Dec 4 11:35:45 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Mon, 4 Dec 2000 11:35:45 GMT Subject: MEME Message-ID: <200012041135.LAA24395@tin.hgmp.mrc.ac.uk> I've put in a fix for this. There is a new MEME tarball on the ftp server under the same name as before. I'm intrigued about the separate LDFLAGS in AJAX for FreeBSD. As far as I know the ajax configure hasn't changed in many months. If you can get back to me with more complete error msgs I can take a look. btw: I am on holiday so apologies if the response time to queries is slow. Alan From johann at egenetics.com Mon Dec 4 12:55:47 2000 From: johann at egenetics.com (Johann Visagie) Date: Mon, 4 Dec 2000 14:55:47 +0200 Subject: MEME In-Reply-To: <3A2B4DE5.BF66C9D9@genprofile.com>; from bauer@genprofile.com on Mon, Dec 04, 2000 at 08:55:17AM +0100 References: <3A2B2C8B.6030602@earthling.net> <3A2B4DE5.BF66C9D9@genprofile.com> Message-ID: <20001204145547.E9796@fling.sanbi.ac.za> David Bauer on 2000-12-04 (Mon) at 08:55:17 +0100: > > I'm getting the same errors when building MEME on FreeBSD, and a new > problem with EMBOSS-1.8.0 itself: > Configure writes wrong LDFLAGS in the ajax/Makefile. What I get there is > "-no-undefined" which results in failing to find the libs. > After changing this to -L/usr/local/lib gcc is happy again. Which version of FreeBSD are you building on? I'm constantly building EMBOSS on FreeBSD - several builds are usually required every time I change anything to the FreeBSD EMBOSS port - and I've not seen the build breaking, ever. (Though I'm doing another build now to be sure.) I do all my development and testing on 5.0-CURRENT these days, though. BTW, the FreeBSD EMBOSS port now includes the EMBASSY applications MSE, PHYLIP and TOPO. Upon installation the user is given an ncurses-based full-screen menu in order to decide which of them to install. I'll add MEME to the port soon as well, and EMNU when it's available. -- Johann From coss at cnb.uam.es Tue Dec 5 11:03:13 2000 From: coss at cnb.uam.es (=?ISO-8859-1?Q?Carlos_Oscar_S=E1nchez_Sorzano?=) Date: Tue, 5 Dec 2000 12:03:13 +0100 Subject: Hello - anybody out there? In-Reply-To: Message-ID: Hello, On Fri, 1 Dec 2000, Robert Milius wrote: > Hello, > > It looks like there are several efforts underway: > > http://www.uk.embnet.org/Software/EMBOSS//Doc/interfaces.html > > for example, coilmate looks like a non-www gui interface > being developed though I don't know how far along they are. > > -bob The colimate interface is going on, there are still several things that must be worked out inside Colimate and then the translation of the ACD files should not be a big problem. I hope that it can be ready in 2 or 3 months. Carlos Oscar. > On Sat, 2 Dec 2000, Philipp Pagel wrote: > > > Hi! > > > > I apologise for this OT posting but I was really wondering if this is a > > problem on my side, or if there IS no traffic on this list... > > > > Anyway: I just downloaded EMBOSS 1.8 on my SUSE LINUX box and started to > > play with it. I really liked what I have seen so far. > > Only the lack of any GUI wrapper for small and dirty jobs is a pitty. > > OK - www interfaces - but I really don't like them. > > > > That makes me wonder if anybody knows about an ongoing project for a > > GUI for EMBOSS implemented in C or whatever. I am not a big coding guru, > > but I might be interested in participating if I can find a little > > time... > > > > cu > > Philipp > > > > -- > > Dr. Philipp Pagel > > Cellular and Molecular Physiology phone: (203) 785-6835 > > SHM BE-30 > > Yale University > > 333 Cedar ST > > New Haven, CT 06520 > > > > > > Robert P. Milius, Ph.D. 612-626-2771 (office) > Basic Sciences Computing Laboratory 612-625-4433 (fax) > University of Minnesota Supercomputing Institute milius at msi.umn.edu > for Digital Simulation and Advanced Computation > > ----------------------------------------------------------------------------- Carlos Oscar S?nchez Sorzano e-mail: coss at cnb.uam.es Unidad de Bioinform?tica http://biocomp.cnb.uam.es Centro Nacional de Biotecnolog?a (CSIC) Campus Universidad Autonoma (Cantoblanco) Tlf: 34-91-585 4683 28049 MADRID (SPAIN) Fax: 34-91-585 4506 ----------------------------------------------------------------------------- From starksb at ebi.ac.uk Tue Dec 5 17:01:27 2000 From: starksb at ebi.ac.uk (David Starks-Browning) Date: Tue, 5 Dec 2000 17:01:27 +0000 Subject: any success with gcc-2.95.2 on Digital Unix? Message-ID: <1188-Tue05Dec2000170127+0000-starksb@ebi.ac.uk> Greeting EMBOSS users, Has anyone successfully built EMBOSS with gcc-2.95.2 on Digital Unix? When I try it, I get syntax errors in ajax/ajfmt.c wherever var_arg is used. It compiles fine with gcc-2.95.2 on other platforms (including IRIX and Linux), so it's probably not a problem with EMBOSS, except possibly via autoconf. Also, the Digital cc build is fine. This is with EMBOSS-1.8.0, though I have always had this problem (though I do not check it regularly). Before I investigate further (it's probably a gcc bug), I thought I would ask if others have had the same experience, in case it's just a problem with my gcc installation. Thanks for your help. Regards, David ------------------------------------------------------------------- David Starks-Browning | starksb at ebi.ac.uk EMBL Outstation -- | The European Bioinformatics Institute | Wellcome Trust Genome Campus | tel: +44 (1223) 494 616 Hinxton, Cambridge, CB10 1SD, UK | fax: +44 (1223) 494 468 ------------------------------------------------------------------- From roels at mpi.com Thu Dec 14 21:16:09 2000 From: roels at mpi.com (Steve Roels) Date: Thu, 14 Dec 2000 16:16:09 -0500 Subject: use of full genbank style ids Message-ID: <3A393899.9D2656EF@mpi.com> Hello, Anyone know if there is a way to force the use of full genbank-style sequence identifiers in output files? for example: >gi|12345|gb|AC00123.4|HUDDR GGCGCGCCG... The id used is either "gi" (if fasta format is specified - or no format is specified) or "gb|AC00123.4|HUDDR" (if ncbi format is specified). In short (and to be more general), what I want is to have everything up to the first white-space (i.e. including vertical bars,colons,etc) to be treated as the id. Thanks, -Steve -- ***************************************************************** Steve Roels, Ph.D. Scientist - Computational Biology Phone: (617) 761-6820 Millennium Pharmaceuticals, Inc. FAX: (617) 577-3568 640 Memorial Drive Email: roels at mpi.com Cambridge, MA 02139-4815 ***************************************************************** From Peter.Rice at uk.lionbioscience.com Fri Dec 15 09:50:48 2000 From: Peter.Rice at uk.lionbioscience.com (Peter Rice) Date: Fri, 15 Dec 2000 09:50:48 +0000 Subject: use of full genbank style ids References: <3A393899.9D2656EF@mpi.com> Message-ID: <3A39E978.46E7EBF6@lionbio.co.uk> Steve Roels wrote: > > Anyone know if there is a way to force the use of full genbank-style sequence identifiers > in output files? > > >gi|12345|gb|AC00123.4|HUDDR > GGCGCGCCG... > > The id used is either "gi" (if fasta format is specified - or no format is specified) or > "gb|AC00123.4|HUDDR" (if ncbi format is specified). > > In short (and to be more general), what I want is to have everything up to the first > white-space (i.e. including vertical bars,colons,etc) to be treated as the id. Possible - by defining a new format. Not a big code change. 'GenBank' is of course the 'wrong' name - as we use that for the CODATA format GENBANK files. This is really NCBI's blast version of the FASTA format. Any suggestions for a format name? You want to include the GI number in parsing, and also pick up the sequence version rather than just the accession number. One question would be - what would you like to use as a filename on output? Unix will not be happy with those '|' characters in a filename, so we would normally trim it back to the ID at the end. I guess the '|' could also break future extensions to the USA syntax if you plan to use these IDs in USAs. We already use '|' at the end to pipe application output (perl style). We could, in theory, use SRS syntax to offer alternative IDs or accession numbers. For example, SRS accepts swissprot-id:amic_ecoli|amic_pseae|amic_strpn and returns 3 entries. Any takers for this syntax in EMBOSS? -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From roels at mpi.com Fri Dec 15 15:07:44 2000 From: roels at mpi.com (Steve Roels) Date: Fri, 15 Dec 2000 10:07:44 -0500 Subject: use of full genbank style ids References: <3A393899.9D2656EF@mpi.com> <3A39E978.46E7EBF6@lionbio.co.uk> Message-ID: <3A3A33C0.BB28593A@mpi.com> Peter et al, Thanks for the quick reply. A few more comments follow. Peter Rice wrote: > > Steve Roels wrote: > > > > Anyone know if there is a way to force the use of full genbank-style sequence identifiers > > in output files? > > > > >gi|12345|gb|AC00123.4|HUDDR > > GGCGCGCCG... > > > > The id used is either "gi" (if fasta format is specified - or no format is specified) or > > "gb|AC00123.4|HUDDR" (if ncbi format is specified). > > > > In short (and to be more general), what I want is to have everything up to the first > > white-space (i.e. including vertical bars,colons,etc) to be treated as the id. > > Possible - by defining a new format. Not a big code change. > > 'GenBank' is of course the 'wrong' name - as we use that for the CODATA > format GENBANK files. This is really NCBI's blast version of the FASTA > format. Any suggestions for a format name? Yes - I should have been more specific. I meant NCBI's style for fasta header ids. Generally: databasetag|id(|possiblymorealiasesorids) and (to be more general still, the ":" equivalent) databasetag:id(:possiblymorealiasesorids) Note to that it could be treated as a two step process: (1) To handle ids most generally, have a format that grabs everything up to the first white space as an id, including delimiters like '|' and ":". You need not try to extract the elements of the id (gid,accession,version,locus for genbank fasta ids for example). Here you leave interpretation of the full id to the user - you just provide a way to pass ids intact from the input file to the output file. This would work for those ( hypothetically speaking :) ) that use the ">dbtag|id" or ">dbtag:id" structure for there own data. Even if I converted an id like "mydb|12345" to "mydb:12345" and specified fasta format, the dbtag is dropped in the output, rendering the id in the output potentially ambiguous. (2) If desired (I don't really need it), expand on #1 (as the "ncbi" format seem to try to do) so that, for example, "sp|P12345" would be recognized as swissprot entry with accession P12345, and "gi|12345|gb|AC00123.4|HUDDR" would be recognized as genbank entry with gid 12345, accession AC00123, version 4, and locus HUDDR. The parsed accessions,locus names,gids, etc could then be used in some contexts. But even here, I'd like the option of putting the full id (including database/source tag) in the output. > > You want to include the GI number in parsing, and also pick up the sequence > version rather than just the accession number. > > One question would be - what would you like to use as a filename on output? > Unix will not be happy with those '|' characters in a filename, so we > would normally trim it back to the ID at the end. I agree this is a problem with the use of "|" as a delimiter. In naming files, we've typically resorted to substituting another character (e.g. "_") for "|" to generate files like: gi_12345_gb_AC00123.4_HUDDR.output or more simply (since the aliases/alt_ids are not really needed): gi_12345.output The key is to have the full id in the output file, and a unique name for the output file. Using just 12345.output for the file, or "12345" in that output file, could be problematic if you have a sequence with id 12345 from more than one database/source. > > I guess the '|' could also break future extensions to the USA syntax if you > plan to use these IDs in USAs. We already use '|' at the end to pipe > application output (perl style). We could, in theory, use SRS syntax > to offer alternative IDs or accession numbers. For example, SRS accepts > swissprot-id:amic_ecoli|amic_pseae|amic_strpn and returns 3 entries. > Any takers for this syntax in EMBOSS? Obviously, I wouldn't want to wreak havoc with the large body of code already in place or envisioned. But if its a simple new format... Thanks again, -Steve > > -- > ------------------------------------------------ > Peter Rice, LION Bioscience Ltd, Cambridge, UK > peter.rice at uk.lionbioscience.com +44 1223 224723 -- ***************************************************************** Steve Roels, Ph.D. Scientist - Computational Biology Phone: (617) 761-6820 Millennium Pharmaceuticals, Inc. FAX: (617) 577-3568 640 Memorial Drive Email: roels at mpi.com Cambridge, MA 02139-4815 *****************************************************************