From lasergene at gmail.com Mon Aug 7 23:10:05 2006 From: lasergene at gmail.com (Kevin Hwang) Date: Tue, 8 Aug 2006 11:10:05 +0800 Subject: [EMBOSS] EMBOSS Digest, Vol 13, Issue 4 In-Reply-To: References: Message-ID: <3d6c72510608072010h63a8b123p8d3e86e6da1fef72@mail.gmail.com> Hi, Everyone, I am learning EMBOSSwin(2.10.0-win-0.8) by myself recently. But a problem puzzled me when I want to align mutiple sequences. I used the command "emma", it can't work. I don't know why and how to resolve it. Does anyone help me? many thanks. Kevin Hwang. From ajb at ebi.ac.uk Tue Aug 8 06:00:59 2006 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Tue, 8 Aug 2006 11:00:59 +0100 (BST) Subject: [EMBOSS] Antwort: Re: EMBOSS Digest, Vol 13, Issue 4 In-Reply-To: References: <3d6c72510608072010h63a8b123p8d3e86e6da1fef72@mail.gmail.com> Message-ID: <43156.81.98.244.247.1155031259.squirrel@webmail.ebi.ac.uk> Hello David, > 2) > Unfortunately this won't help much, because there seems to be a problem > with emma also in the new windows version. I can't reproduce the problem. > emma is not a full application, but only an interface to the multiple > alignment program clustalW. > The current windows version of EMBOSS contains an clustalw executable, but > this doesn't work. (Error message I get: "The system cannot execute the > specified program"). Well that's definitely a Microsoft error message rather than an EMBOSS one. I have tried the clustalw.exe supplied with EMBOSS-MS on a few Windows setups on a range of machines just now. None showed that error. Admittedly some of the machines required the vcredist_x86.exe Visual C/C++ 2005 runtime libraries added but that was mentioned in the announcement (and I've just put a README.win on the ftp server saying the same). Besides, that would usually give a "Missing DLL" error, not the "Cannot Execute" one. I do find it odd that clustalw.exe gives that error but the emboss applications do not: they were all built using the same compiler on the same machine. DependencyWalker (http://www.dependencywalker.com) shows that the required modules on XP for clustalw are kernel32.dll, msvcr80.dll, msvcrt.dll and ntdll.dll. You could try installing Dependencywalker and seeing whether it detects any missing modules for clustalw on your system. Does the problem occur on your home XP installations, your Schering installation or both? > I replaced it with the XP executable from > ftp://ftp.ebi.ac.uk/pub/software/dos/clustalw/ but now I'm getting a > different problem. > The clustalw used directly runs without problem. But if called from emma > it complains: > CLUSTAL W (1.83) Multiple Sequence Alignments > Error: unknown option /-infile=00002432A > Error: Failed to open filename '00002432B' > Problem writing out EMBOSS alignment file > clustalw needs just /infile= and not /-infile= Yes, it would do that :-) Versions of clustalw for Windows found on the network usually do not have the UNIX-style command line. You must use the clustalw.exe supplied with EMBOSS-MS which does have the UNIX command line. > Btw. I could not reproduce the Path overwriting on any generic XP (Pro or > Home) so it has something to do with our local XP installtion but I could > not find the reason so far. I'm still intrigued by that one. I expect that you've checked that there isn't another program called setenv.exe on the system? ATB Alan From David.Bauer at SCHERING.DE Tue Aug 8 02:19:00 2006 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Tue, 8 Aug 2006 08:19:00 +0200 Subject: [EMBOSS] Antwort: Re: EMBOSS Digest, Vol 13, Issue 4 In-Reply-To: <3d6c72510608072010h63a8b123p8d3e86e6da1fef72@mail.gmail.com> Message-ID: Hi, 1) If you just start with emboss on windows, why don't you try the latest version 4.0.0 ? You can find it in ftp://emboss.open-bio.org/pub/EMBOSS/windows/. 2) Unfortunately this won't help much, because there seems to be a problem with emma also in the new windows version. emma is not a full application, but only an interface to the multiple alignment program clustalW. The current windows version of EMBOSS contains an clustalw executable, but this doesn't work. (Error message I get: "The system cannot execute the specified program"). I replaced it with the XP executable from ftp://ftp.ebi.ac.uk/pub/software/dos/clustalw/ but now I'm getting a different problem. The clustalw used directly runs without problem. But if called from emma it complains: CLUSTAL W (1.83) Multiple Sequence Alignments Error: unknown option /-infile=00002432A Error: Failed to open filename '00002432B' Problem writing out EMBOSS alignment file clustalw needs just /infile= and not /-infile= So I guess Alan can resolve what's going on here ;-) Ciao, David. Btw. I could not reproduce the Path overwriting on any generic XP (Pro or Home) so it has something to do with our local XP installtion but I could not find the reason so far. emboss-bounces at lists.open-bio.org schrieb am 08/08/2006 05:10:05: > Hi, Everyone, > I am learning EMBOSSwin(2.10.0-win-0.8) by myself recently. But a problem > puzzled me when I want to align mutiple sequences. I used the command > "emma", it can't work. I don't know why and how to resolve it. Does anyone > help me? many thanks. > > Kevin Hwang. > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From ajb at ebi.ac.uk Tue Aug 8 08:36:31 2006 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Tue, 8 Aug 2006 13:36:31 +0100 (BST) Subject: [EMBOSS] Antwort: Re: EMBOSS Digest, Vol 13, Issue 4 In-Reply-To: References: <43156.81.98.244.247.1155031259.squirrel@webmail.ebi.ac.uk> Message-ID: <52915.81.98.244.247.1155040591.squirrel@webmail.ebi.ac.uk> Hello David, > It was the missing msvcr80.dll. I have the older version msvcr70.dll. > The only idea I have why there was no "dll not found" error is, that > windows tries > to fix the missing dll by falling back to the older version and clustalw > then > runs into trouble ? That is good to know. Thanks. The installer does have the capability of safely (it says) adding system DLLs to the Windows system directory but I'm a little wary of doing that at the moment. There dragons may live. For the alpha test, at least, it is probably better that people install vcredist_x86.exe as necessary. Thanks for the Path info. Curious indeed. Alan From David.Bauer at SCHERING.DE Tue Aug 8 07:57:48 2006 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Tue, 8 Aug 2006 13:57:48 +0200 Subject: [EMBOSS] Antwort: Re: EMBOSS Digest, Vol 13, Issue 4 In-Reply-To: <43156.81.98.244.247.1155031259.squirrel@webmail.ebi.ac.uk> Message-ID: Hello Alan, > DependencyWalker (http://www.dependencywalker.com) shows that the That's a nice tool ! > required modules on XP for clustalw are kernel32.dll, msvcr80.dll, > msvcrt.dll and ntdll.dll. You could try installing Dependencywalker > and seeing whether it detects any missing modules for clustalw on > your system. It was the missing msvcr80.dll. I have the older version msvcr70.dll. The only idea I have why there was no "dll not found" error is, that windows tries to fix the missing dll by falling back to the older version and clustalw then runs into trouble ? > > Btw. I could not reproduce the Path overwriting on any generic XP (Pro or > > Home) so it has something to do with our local XP installtion but I could > > not find the reason so far. > > I'm still intrigued by that one. I expect that you've checked that > there isn't another program called setenv.exe on the system? The only special thing is, that I have a Path under user variables AND under system variables. But I tried to reproduce this situation on another machine and the emboss dir was correctly appended there to the system Path. Curious. Thanks, David. From hrh at sanger.ac.uk Fri Aug 11 08:54:09 2006 From: hrh at sanger.ac.uk (Hans Rudolf Hotz) Date: Fri, 11 Aug 2006 13:54:09 +0100 (BST) Subject: [EMBOSS] display of long ensembl and vega identifiers in alignments In-Reply-To: References: Message-ID: Hi ensembl and vega identifiers are very long, and are therefore cut when used in alignment programs like matcher, eg: cbi1b[hrh]59: matcher pep1 pep2 stdout Finds the best local alignments between two sequences ######################################## # Program: matcher # Rundate: Fri Aug 11 2006 13:45:51 # Align_format: markx0 # Report_file: stdout ######################################## #======================================= # # Aligned_sequences: 2 # 1: OTTHUMT00000072262 # 2: ENST00000216277 # Matrix: EBLOSUM62 # Gap_penalty: 14 # Extend_penalty: 4 # # Length: 745 # Identity: 745/745 (100.0%) # Similarity: 745/745 (100.0%) # Gaps: 0/745 ( 0.0%) # Score: 3818 # # #======================================= 10 20 30 40 50 OTTHUM MPFPVTTQGSQQTQPPQKHYGITSPISLAAPKETDCVLTQKLIETLKPFG :::::::::::::::::::::::::::::::::::::::::::::::::: ENST00 MPFPVTTQGSQQTQPPQKHYGITSPISLAAPKETDCVLTQKLIETLKPFG 10 20 30 40 50 A few months back, I played arround with the source code and changed one of the library files (ajalign.c). This now allows the display of up to 20 characters, by using a new output format "pairln" for sequence alignment programs, like matcher or needle. This is in comparison to the default which displays only the first 6 characters, or "pair" which displays the first 13 characters, eg: cbi1b[hrh]65: matcher pep1 pep2 stdout -aformat pairln Finds the best local alignments between two sequences ######################################## # Program: matcher # Rundate: Fri Aug 11 2006 13:49:41 # Align_format: pairln # Report_file: stdout ######################################## #======================================= # # Aligned_sequences: 2 # 1: OTTHUMT00000072262 # 2: ENST00000216277 # Matrix: EBLOSUM62 # Gap_penalty: 14 # Extend_penalty: 4 # # Length: 745 # Identity: 745/745 (100.0%) # Similarity: 745/745 (100.0%) # Gaps: 0/745 ( 0.0%) # Score: 3818 # # #======================================= OTTHUMT00000072262 1 MPFPVTTQGSQQTQPPQKHYGITSPISLAAPKETDCVLTQKLIETLKPFG 50 |||||||||||||||||||||||||||||||||||||||||||||||||| ENST00000216277 1 MPFPVTTQGSQQTQPPQKHYGITSPISLAAPKETDCVLTQKLIETLKPFG 50 Any chance something like this could make it into the distributed code? Thanks, Hans From pmr at ebi.ac.uk Fri Aug 11 09:53:23 2006 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 11 Aug 2006 14:53:23 +0100 Subject: [EMBOSS] display of long ensembl and vega identifiers in alignments In-Reply-To: References: Message-ID: <44DC8BD3.6080800@ebi.ac.uk> Hans Rudolf Hotz wrote: > A few months back, I played arround with the source code and changed one > of the library files (ajalign.c). This now allows the display of up to 20 > characters, by using a new output format "pairln" for sequence alignment > programs, like matcher or needle. This is in comparison to the default > which displays only the first 6 characters, or "pair" which displays the > first 13 characters, eg: We can make the ID arbitrarily long for a "new" alignment format. We will need formats similar to the existing matcher and needle outputs to avoid breaking too many existing parsers (I remember when NCBI changed the use of a blank at the start of each line of blast output and almost all parsers had to change). The formats are easy to make (as you found out) from the existing ones. We need to decide what to do with the standard alignment formats that have 6 characters in their definition (I assume this goes back to the days of PIR database identifiers when FASTP was first written). As we cannot fit many of the existing identifiers, we can make up unique identifiers for these (truncate the identifier, and make the names unique if they match). Or, should we change the existing formats to allow longer IDs? What do the authors of parsers think? regards, Peter From golharam at umdnj.edu Fri Aug 11 13:51:23 2006 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 11 Aug 2006 13:51:23 -0400 Subject: [EMBOSS] 404 error on web site Message-ID: <007a01c6bd6e$c29cb560$2f01a8c0@GOLHARMOBILE1> I'm viewing http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/index.html. I click on the "EMBASSY applications" link and I get a 404 error. From golharam at umdnj.edu Fri Aug 11 15:47:46 2006 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 11 Aug 2006 15:47:46 -0400 Subject: [EMBOSS] Compiling EMNU fails with EMBOSS 4.0.0 Message-ID: <008201c6bd7f$04ac6120$2f01a8c0@GOLHARMOBILE1> So I'm recompiling the EMNU package to link with EMBOSS 4.0.0 and I'm getting some compiler errors that I don't get with EMBOSS 3.0.0: emnu.c: In function `populate_program_menus': emnu.c:1307: `GPnode' undeclared (first use in this function) emnu.c:1307: (Each undeclared identifier is reported only once emnu.c:1307: for each function it appears in.) emnu.c:1307: syntax error before "gl" emnu.c:1314: `gl' undeclared (first use in this function) emnu.c:1315: warning: `ajStrLen' is deprecated (declared at /usr/include/ajstr.h:591) emnu.c:1315: warning: `ajStrLen' is deprecated (declared at /usr/include/ajstr.h:591) emnu.c:1322: warning: `ajStrLen' is deprecated (declared at /usr/include/ajstr.h:591) emnu.c:1324: warning: `ajStrLen' is deprecated (declared at /usr/include/ajstr.h:591) emnu.c:1325: warning: `ajStrStr' is deprecated (declared at /usr/include/ajstr.h:644) emnu.c:1327: warning: `ajStrStr' is deprecated (declared at /usr/include/ajstr.h:644) emnu.c:1330: warning: `ajStrStr' is deprecated (declared at /usr/include/ajstr.h:644) emnu.c:1330: warning: `ajStrStr' is deprecated (declared at /usr/include/ajstr.h:644) emnu.c: In function `populate_menu': emnu.c:1356: `GPnode' undeclared (first use in this function) emnu.c:1356: syntax error before "gl" emnu.c:1373: `gl' undeclared (first use in this function) emnu.c:1384: warning: `ajStrStr' is deprecated (declared at /usr/include/ajstr.h:644) emnu.c:1422: warning: `ajStrAssC' is deprecated (declared at /usr/include/ajstr.h:538) emnu.c:1424: too few arguments to function `embGrpKeySearchProgs' make[1]: *** [emnu.o] Error 1 make[1]: Leaving directory `/usr/src/redhat/BUILD/EMNU-1.05/source' make: *** [all-recursive] Error 1 Is anyone else able to compile EMNU using EMBOSS 4? Ryan From ajb at ebi.ac.uk Fri Aug 11 17:59:00 2006 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Fri, 11 Aug 2006 22:59:00 +0100 (BST) Subject: [EMBOSS] Compiling EMNU fails with EMBOSS 4.0.0 In-Reply-To: <008201c6bd7f$04ac6120$2f01a8c0@GOLHARMOBILE1> References: <008201c6bd7f$04ac6120$2f01a8c0@GOLHARMOBILE1> Message-ID: <36305.81.98.244.247.1155333540.squirrel@webmail.ebi.ac.uk> Each time a new EMBOSS version is released the EMBASSY packages are reconstructed: the EMBASSY packages are specific to a given release. You're trying to compile the EMNU supplied with EMBOSS 3.0.0 on EMBOSS 4.0.0. You need to download EMNU again from the ftp server. The version numbers of the EMBASSY packages reflects their internal functionality and not the version of the main package they are linked against. As this seems to be a common gotcha we'll think of altering this for future releases. We will also consider removing EMNU from future releases. It has been superseded by lots of good GUIs out there. HTH Alan From golharam at umdnj.edu Sun Aug 13 20:33:06 2006 From: golharam at umdnj.edu (Ryan Golhar) Date: Sun, 13 Aug 2006 20:33:06 -0400 Subject: [EMBOSS] Compiling EMNU fails with EMBOSS 4.0.0 In-Reply-To: <36305.81.98.244.247.1155333540.squirrel@webmail.ebi.ac.uk> Message-ID: <002901c6bf39$37e0fa90$2f01a8c0@GOLHARMOBILE1> It might not be a bad idea, or else there is no indication that a new version is available... -----Original Message----- From: ajb at ebi.ac.uk [mailto:ajb at ebi.ac.uk] Sent: Friday, August 11, 2006 5:59 PM To: golharam at umdnj.edu Cc: emboss at lists.open-bio.org Subject: Re: [EMBOSS] Compiling EMNU fails with EMBOSS 4.0.0 Each time a new EMBOSS version is released the EMBASSY packages are reconstructed: the EMBASSY packages are specific to a given release. You're trying to compile the EMNU supplied with EMBOSS 3.0.0 on EMBOSS 4.0.0. You need to download EMNU again from the ftp server. The version numbers of the EMBASSY packages reflects their internal functionality and not the version of the main package they are linked against. As this seems to be a common gotcha we'll think of altering this for future releases. We will also consider removing EMNU from future releases. It has been superseded by lots of good GUIs out there. HTH Alan From rls at ebi.ac.uk Mon Aug 14 03:28:11 2006 From: rls at ebi.ac.uk (Rodrigo Lopez) Date: Mon, 14 Aug 2006 08:28:11 +0100 Subject: [EMBOSS] Compiling EMNU fails with EMBOSS 4.0.0 In-Reply-To: <002901c6bf39$37e0fa90$2f01a8c0@GOLHARMOBILE1> References: <002901c6bf39$37e0fa90$2f01a8c0@GOLHARMOBILE1> Message-ID: <44E0260B.7020100@ebi.ac.uk> FYI: Des Higgins is planning to release a new version of clustalw ca. end 2006. R:) Ryan Golhar wrote: > It might not be a bad idea, or else there is no indication that a new > version is available... > > -----Original Message----- > From: ajb at ebi.ac.uk [mailto:ajb at ebi.ac.uk] > Sent: Friday, August 11, 2006 5:59 PM > To: golharam at umdnj.edu > Cc: emboss at lists.open-bio.org > Subject: Re: [EMBOSS] Compiling EMNU fails with EMBOSS 4.0.0 > > > Each time a new EMBOSS version is released the EMBASSY packages are > reconstructed: the EMBASSY packages are specific to a given release. > > You're trying to compile the EMNU supplied with EMBOSS 3.0.0 on EMBOSS > 4.0.0. You need to download EMNU again from the ftp server. > > The version numbers of the EMBASSY packages reflects their internal > functionality and not the version of the main package they are linked > against. As this seems to be a common gotcha we'll think of altering > this for future releases. > > We will also consider removing EMNU from future releases. It has been > superseded by lots of good GUIs out there. > > HTH > > Alan > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From maoj at helix.nih.gov Mon Aug 14 15:23:04 2006 From: maoj at helix.nih.gov (Jean Mao) Date: Mon, 14 Aug 2006 15:23:04 -0400 Subject: [EMBOSS] Problem installing EMBOSS-4.0.0 on SGI system Message-ID: <000001c6bfd7$11112d10$be4de780@CIT.NIH.GOV> Hi, I received the error message below while trying to install the package on our SGI running irix 6.5.28. We successfully installed version 3.0.0 previously without problem. Could anyone help me ? Thank you very much in advance! % make ??? ??. /bin/sh ../libtool --tag=CC --mode=link cc -Wl,-LD_MSG:off=85:off=84:off=16:off=134 -O3 -o aaindexextract aaindexextract.o ../nucleus/libnucleus.la ../ajax/libajaxg.la ../ajax/libajax.la ../plplot/libplplot.la -L/usr/lib -lX11 -lm mkdir .libs cc -Wl,-LD_MSG:off=85:off=84:off=16:off=134 -O3 -o .libs/aaindexextract aaindexextract.o ../nucleus/.libs/libnucleus.so ../ajax/.libs/libajaxg.so ../ajax/.libs/libajax.so ../plplot/.libs/libplplot.so -L/usr/lib -lX11 -lm -Wl,-rpath -Wl,/usr/localapps/EMBOSS-4.0.0/lib ld32: FATAL 12 : Expecting n32 objects: /usr/lib/crt1.o is o32. *** Error code 2 (bu21) *** Error code 1 (bu21) *** Error code 1 (bu21) % Jean From ajb at ebi.ac.uk Mon Aug 14 17:01:59 2006 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Mon, 14 Aug 2006 22:01:59 +0100 (BST) Subject: [EMBOSS] Problem installing EMBOSS-4.0.0 on SGI system In-Reply-To: <000001c6bfd7$11112d10$be4de780@CIT.NIH.GOV> References: <000001c6bfd7$11112d10$be4de780@CIT.NIH.GOV> Message-ID: <55530.81.98.244.247.1155589319.squirrel@webmail.ebi.ac.uk> Hi Jean, That error usually suggests that the linker would have much preferred to be looking in /usr/lib32. Did you use the --with-sgiabi configuration switch? That would usually make sure that the library path is set up correctly. The syntax is --with-sgiabi=xxxxx where xxxxx is: n32m3 n32m4 64m3 or 64m4 Do a "make clean" before configuring again. Alan From golharam at umdnj.edu Thu Aug 17 15:14:37 2006 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 17 Aug 2006 15:14:37 -0400 Subject: [EMBOSS] EMBOSS 4.0.0 RPMs Message-ID: <023001c6c231$626351a0$2f01a8c0@GOLHARMOBILE1> I've built RPMs for EMBOSS 4.0.0 and related applications. Is there a place I can put them formally? They are available from http://serine.umdnj.edu/~golharam/biorpms Ryan From jison at ebi.ac.uk Fri Aug 18 05:39:27 2006 From: jison at ebi.ac.uk (Jon Ison) Date: Fri, 18 Aug 2006 10:39:27 +0100 (BST) Subject: [EMBOSS] EMBOSS 4.0.0 RPMs In-Reply-To: <023001c6c231$626351a0$2f01a8c0@GOLHARMOBILE1> References: <023001c6c231$626351a0$2f01a8c0@GOLHARMOBILE1> Message-ID: <1310.84.92.187.247.1155893967.squirrel@webmail.ebi.ac.uk> Thanks Ryan I can put them on the EMBOSS ftp site and point to them from the website, on Monday, if that would suit. I'll let you know where the links are. Cheers Jon > I've built RPMs for EMBOSS 4.0.0 and related applications. Is there a > place I can put them formally? > > They are available from http://serine.umdnj.edu/~golharam/biorpms > > Ryan > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From haruosuz at yahoo.co.jp Sun Aug 20 03:38:40 2006 From: haruosuz at yahoo.co.jp (haruosuz at yahoo.co.jp) Date: Sun, 20 Aug 2006 00:38:40 -0700 Subject: [EMBOSS] emboss_4.0.0-2 Message-ID: <4813B756-1E2C-4E77-A491-A5CB4E81EDD2@yahoo.co.jp> Dear Sir: I installed emboss_4.0.0-2, but any commands (e.g., wossname) did not work, as follows: -------------------------------------------- $fink install emboss Information about 5218 packages read in 1 seconds. The following package will be installed or updated: emboss /sw/bin/dpkg-lockwait -i /sw/fink/dists/unstable/main/binary-darwin- i386/sci/emboss_4.0.0-2_darwin-i386.deb $wossname dyld: Library not loaded: /usr/local/lib/libnucleus.3.dylib Referenced from: /usr/local/bin/wossname Reason: image not found Trace/BPT trap -------------------------------------------- [About my Mac] Mac OS X 10.4.6; Darwin 8.6.1; MacBookPro1,1; Intel Core Duo I am looking forward to hearing from you. Sincerely yours, Haruo Suzuki -------------------------------------- Let's start Yahoo! Auction - Free Campaign Now! http://pr.mail.yahoo.co.jp/auction/ From kvddrift at earthlink.net Sun Aug 20 05:29:00 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sun, 20 Aug 2006 05:29:00 -0400 Subject: [EMBOSS] emboss_4.0.0-2 In-Reply-To: <4813B756-1E2C-4E77-A491-A5CB4E81EDD2@yahoo.co.jp> References: <4813B756-1E2C-4E77-A491-A5CB4E81EDD2@yahoo.co.jp> Message-ID: <63DDA3CE-E18A-4373-A518-BA1C168311FA@earthlink.net> On Aug 20, 2006, at 3:38 AM, haruosuz at yahoo.co.jp wrote: > dyld: Library not loaded: /usr/local/lib/libnucleus.3.dylib You seem to have another emboss installation outside fink. Remove that first, and then try again. You may have to rebuild emboss to get it to work. - Koen. From sea99.wang at gmail.com Wed Aug 23 09:01:20 2006 From: sea99.wang at gmail.com (Sea) Date: Wed, 23 Aug 2006 21:01:20 +0800 Subject: [EMBOSS] Installation problems of EMBOSS explorer In-Reply-To: <4f3a50530608230324r886b255lebbe7ab5fe3ae873@mail.gmail.com> References: <4f3a50530608230324r886b255lebbe7ab5fe3ae873@mail.gmail.com> Message-ID: <4f3a50530608230601x4bf1a55cwa44d3dc9605a850e@mail.gmail.com> Hi, This is my first time to install EMBOSS explorer, but I couldn't install successfully. It showed some error messages and seem problems about the perl module. Because I used a non-root-privilege account to do the thing and installed a non-default directory, I'm not sure whether it caused that results. Would any experienced friends tell me some hints? Thanks a lot! :-) From maoj at helix.nih.gov Wed Aug 23 10:19:42 2006 From: maoj at helix.nih.gov (Jean Mao) Date: Wed, 23 Aug 2006 10:19:42 -0400 Subject: [EMBOSS] Question regarding 'showdb' in EMBOSS Message-ID: <000001c6c6bf$2d577f80$be4de780@CIT.NIH.GOV> Hi, I have a question hopefully someone could help me. We have a very hetergenous system which are composed of different platforms. They can all access a shared area where I installed EMBOSS 4.0. The databases are sync'd from area A (both read and writable) to area B (Readable but not writable). When I run 'showdb' on platform A which access databases in area A, I can see the output just fine without any strange message. However, when I run 'showdb' on platform B can access databases in area B, I saw % showdb Displays information on the currently available databases # Name Type ID Qry All Comment # ============ ==== == === === ======= monthaa P OK OK OK - monthnt N OK OK OK - EMBOSS An error in ajfile.c at line 1272: File close problem in fileClose I tried: % showdb -debug But saw the same thing as above without extra information: Displays information on the currently available databases # Name Type ID Qry All Comment # ============ ==== == === === ======= monthaa P OK OK OK - monthnt N OK OK OK - EMBOSS An error in ajfile.c at line 1272: File close problem in fileClose I am not sure why I see this error although the databases were listed just fine. The only thing I can think of is that the databases are located differently. Both .embossrc file and emboss.default file are located in shared area. Could someone give me some hint where this error might come from? Thank you very much! Jean From pmr at ebi.ac.uk Wed Aug 23 11:14:40 2006 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Wed, 23 Aug 2006 16:14:40 +0100 (BST) Subject: [EMBOSS] Question regarding 'showdb' in EMBOSS In-Reply-To: <000001c6c6bf$2d577f80$be4de780@CIT.NIH.GOV> References: <000001c6c6bf$2d577f80$be4de780@CIT.NIH.GOV> Message-ID: <4850.86.141.183.154.1156346080.squirrel@webmail.ebi.ac.uk> Hi Jean, > We have a very hetergenous system which are composed of different > platforms. They can all access a shared area where I installed EMBOSS 4.0. > The databases are sync'd from area A (both read and writable) to area B > (Readable but not writable). When I run 'showdb' on platform A which > access databases in area A, I can see the output just fine without any > strange message. However, when I run 'showdb' on platform B can access > databases in area B, I saw > > % showdb > Displays information on the currently available databases > # Name Type ID Qry All Comment > # ============ ==== == === === ======= > monthaa P OK OK OK - > monthnt N OK OK OK - > > EMBOSS An error in ajfile.c at line 1272: > File close problem in fileClose Curious. The error suggests that the fclose call returned an error. We do not trap the exact error. I will look into ways to get a better error report so we can see what the problem is. > I tried: > > % showdb -debug > > But saw the same thing as above without extra information: -debug creates a file (showdb.dbg) with the debug report. It would be helpful if you can send it to me. regards, Peter Rice From golharam at umdnj.edu Wed Aug 23 11:33:08 2006 From: golharam at umdnj.edu (Ryan Golhar) Date: Wed, 23 Aug 2006 11:33:08 -0400 Subject: [EMBOSS] Installation problems of EMBOSS explorer In-Reply-To: <4f3a50530608230601x4bf1a55cwa44d3dc9605a850e@mail.gmail.com> Message-ID: <004501c6c6c9$6f22b6f0$e6028a0a@GOLHARMOBILE1> What are the errors you are getting? -----Original Message----- From: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Sea Sent: Wednesday, August 23, 2006 9:01 AM To: emboss at lists.open-bio.org Subject: [EMBOSS] Installation problems of EMBOSS explorer Hi, This is my first time to install EMBOSS explorer, but I couldn't install successfully. It showed some error messages and seem problems about the perl module. Because I used a non-root-privilege account to do the thing and installed a non-default directory, I'm not sure whether it caused that results. Would any experienced friends tell me some hints? Thanks a lot! :-) _______________________________________________ EMBOSS mailing list EMBOSS at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss From maoj at helix.nih.gov Wed Aug 23 16:40:42 2006 From: maoj at helix.nih.gov (Jean Mao) Date: Wed, 23 Aug 2006 16:40:42 -0400 Subject: [EMBOSS] Question about make use of multiple fields indexing by dbxfasta or dbxflat Message-ID: <000501c6c6f4$66aad770$be4de780@CIT.NIH.GOV> Hello, I need to index swissprot data file from uniprot.org. They have two formats : fasta and flat available. I understand I can specify fields to be indexed. And there are more fields can be specified if using flat file with dbxflat. However, I am not sure how many programs in EMBOSS package will be benefit from specifying extra fields other than acc and id except 'seqret'? Could someone let me know how to find the answer? Thanks you very much in advance. Jean From sea99.wang at gmail.com Thu Aug 24 23:48:37 2006 From: sea99.wang at gmail.com (Sea) Date: Fri, 25 Aug 2006 11:48:37 +0800 Subject: [EMBOSS] Installation problems of EMBOSS explorer In-Reply-To: <004501c6c6c9$6f22b6f0$e6028a0a@GOLHARMOBILE1> References: <4f3a50530608230601x4bf1a55cwa44d3dc9605a850e@mail.gmail.com> <004501c6c6c9$6f22b6f0$e6028a0a@GOLHARMOBILE1> Message-ID: <4f3a50530608242048u7f978211se5df35673cd5a20e@mail.gmail.com> Hi Ryan, Here is the error shown: server: emboss [source/emboss-explorer]> ./install installing EMBOSS Explorer perl modules... Warning: prerequisite Mail::Send failed to load: Can't locate Mail/Send.pm in @INC (@INC contains: /usr/perl5/5.6.1/lib/sun4-solaris-64int /usr/perl5/5.6.1/lib /usr/perl5/site_perl/5.6.1/sun4-solaris-64int /usr/perl5/site_perl/5.6.1 /usr/perl5/site_perl /usr/perl5/vendor_perl/5.6.1/sun4-solaris-64int /usr/perl5/vendor_perl/5.6.1 /usr/perl5/vendor_perl .) at (eval 4) line 3. Warning: prerequisite Parse::RecDescent failed to load: Can't locate Parse/RecDescent.pm in @INC (@INC contains: /usr/perl5/5.6.1/lib/sun4-solaris-64int /usr/perl5/5.6.1/lib /usr/perl5/site_perl/5.6.1/sun4-solaris-64int /usr/perl5/site_perl/5.6.1 /usr/perl5/site_perl /usr/perl5/vendor_perl/5.6.1/sun4-solaris-64int /usr/perl5/vendor_perl/5.6.1 /usr/perl5/vendor_perl .) at (eval 5) line 3. 'PREREQ_FATAL' is not a known MakeMaker parameter name. Writing Makefile for EMBOSS::GUI Manifying blib/man3/EMBOSS::GUI.3 Manifying blib/man3/EMBOSS::GUI::XHTML.3 Manifying blib/man3/EMBOSS::GUI::Conf.3 Manifying blib/man3/EMBOSS::ACD.3 Manifying blib/man3/EMBOSS::GUI.3 Warning: You do not have permissions to install into /usr/perl5/site_perl/5.6.1/sun4-solaris-64int at /usr/perl5/5.6.1/lib/ExtUtils/Install.pm line 85. mkdir /usr/perl5/site_perl/5.6.1/EMBOSS: Permission denied at /usr/perl5/5.6.1/lib/ExtUtils/Install.pm line 138 *** Error code 255 make: Fatal error: Command failed for target `pure_site_install' I guess that I don't have a root privilege so can't access the /usr/perl5 directory. Thus I installed perl 5.8.5 in my folder and then modified the emboss-explorer "Makefile", but still failed. Hope any experienced friends give me some suggestions. :-) Thank you! On 8/23/06, Ryan Golhar wrote: > What are the errors you are getting? > > -----Original Message----- > From: emboss-bounces at lists.open-bio.org > [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Sea > Sent: Wednesday, August 23, 2006 9:01 AM > To: emboss at lists.open-bio.org > Subject: [EMBOSS] Installation problems of EMBOSS explorer > > > Hi, > > This is my first time to install EMBOSS explorer, > but I couldn't install successfully. > > It showed some error messages and seem problems about the perl module. > > Because I used a non-root-privilege account to do the thing and > installed a non-default directory, I'm not sure whether it caused that > results. > > Would any experienced friends tell me some hints? > > Thanks a lot! :-) > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From aengus.stewart at cancer.org.uk Fri Aug 25 04:34:43 2006 From: aengus.stewart at cancer.org.uk (Aengus Stewart) Date: Fri, 25 Aug 2006 09:34:43 +0100 Subject: [EMBOSS] Jemboss - fuzzpro main panel Message-ID: <44EEB623.8050805@cancer.org.uk> Hi, Sorry I have a problem with Jemboss - the panel for fuzzpro only has a box for "input sequence" there is no way to enter a pattern! fuzzpro runs correctly at the command line. Is there a set of files that define the panel interfaces? Have I managed to mangle these or are they wrong? How do I get/build a new set? Aengus -- ----------------------------------------------------------------------- Aengus Stewart Group Leader Bioinformatics and BioStatistics Tel: +44 (0)20 7269 3679 Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK ----------------------------------------------------------------------- This electronic message contains information which may be privileged and confidential. The information is intended to be for the use of the individual(s) or entity named above. Be aware that any third party disclosure, distribution, copying or use of this communication, without prior permission, is strictly prohibited. From tjc at sanger.ac.uk Fri Aug 25 07:36:28 2006 From: tjc at sanger.ac.uk (Tim Carver) Date: Fri, 25 Aug 2006 12:36:28 +0100 Subject: [EMBOSS] Jemboss - fuzzpro main panel In-Reply-To: <44EEB623.8050805@cancer.org.uk> Message-ID: Hi Aengus This is a problem in the current EMBOSS release. I have committed a temporary fix in CVS. Regards Tim On 25/8/06 09:34, "Aengus Stewart" wrote: > Hi, > > Sorry I have a problem with Jemboss - the panel for fuzzpro only has a box for > "input sequence" there is no way to enter a pattern! fuzzpro runs correctly > at the command line. > > Is there a set of files that define the panel interfaces? Have I managed to > mangle these or are they wrong? How do I get/build a new set? > > > Aengus From pmr at ebi.ac.uk Fri Aug 25 09:59:50 2006 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 25 Aug 2006 14:59:50 +0100 Subject: [EMBOSS] EMBOSS 4.0.0 Latest Fixes Message-ID: <44EF0256.1040802@ebi.ac.uk> I have posted some further fixes on the EMBOSS FTP site. None are critical. Users have been reporting interesting bugs. Some were also in release 3.0.0. The fuzznuc, fuzzpro and fuzztran reports were changed in 4.0.0 to always report something. Unfortunately users running searches over the whole database found their output files were very large. We have changed the way reports work as follows: 1. fuzznuc, fuzzpro and fuzztran again report only sequences with hits 2. when a report is closed, a default header and footer are written (solving the problem of empty output files) 3. for sites that had concerns about searches for trivial patterns taking too long and generating too much output, reports have 2 new associated qualifiers. -rmaxall limits the total number of matches reported (fuzznuc, fuzzpro and fuzztran terminate when the limit is reached), -rmaxseq limits the maximum number of hits for one sequence. We also have various fixes for reporting matches on the reverse strand, and for improved parsing of FASTA file IDs. To update your EMBOSS 4.0.0 release, go to: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/ File README.fixes (see below) lists the files and describes the fixes. Copy the files to the indicated directories and reinstall. regards, Peter Rice file README.fixes 25-aug-2006 The files in this directory are bugfix replacements for files in the EMBOSS-4.0.0 distribution. Just drop the replacement files in the location shown and redo the 'make install.' Fix 1. EMBOSS-4.0.0/nucleus/embpatlist.c 31 Jul 2006: Fixes a problem with searching for patterns and regular expression in the reverse strand of nucleotide sequences. The change is to use ajSeqReverseForce (always reverses the sequence provided) instead of ajSeqReverseDo (which only reverses if the reverse flag is set) 9 Aug 2006: Revised to also fix a problem with reverse strand sequence positions. Fix 2. EMBOSS-4.0.0/ajax/ajfile.c 31 Jul 2006: This fixes a bug where deleting the last line of buffered input fails to reset the pointer to the last buffered line. This only affected debug traces. Unfortunately, the ajFileBuffClear function does call the debug trace. In practice we have only seen this bug when processing sequence data in EMBL format from an MRS server. Fix 3. EMBOSS-4.0.0/ajax/ajnam.c 31 Jul 3006: New database access methods MRS and DBFETCH need to be explicitly turned on so that showdb can report them. Fix 4. EMBOSS-4.0.0/ajax/ajseqdb.c 31 Jul 2006: The new MRS access method used a general search. This gave strange results when the ID or accession appeared in any other entry. It appears that MRS can search for id or accession only. This worked on the main MRS server at least. MRS access will be further extended in the next release. Please contact the developers emboss-bug at emboss.open-bio.org if you would like to help test new features in MRS access. 25 Aug 2006: Further change to allow multiple %s replacements in complex URLs for access method URL. Needed for complex SRS queries to resolve EMBL IDs so the following definition can be used for EMBL (warning, the URL may wrap badly in this email!) DB embl [ method: "url" format: "embl" type: "N" url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-noSession+-ascii+-vn+2+-e+[embl-id:%s]|[embl-acc:%s]|([emblidacc-id:%s]>embl)" comment: "EMBL from SRS including old IDs" ] Fix 5. EMBOSS-4.0.0/configure 07 Aug 2006: Fix configuration problem on Intel Mac machines. Make sure this file is executable (chmod 755 configure) after downloading it. Fix 6. EMBOSS-4.0.0/ajax/ajseq.c 09 Aug 2006: Return correct USA for "asis::" sequence input. Fix 7. EMBOSS-4.0.0/emboss/dreg.c 09 Aug 2006: Correct sequence positions on the reverse strand. Fix 8. See Fix 13 Fix 9. See Fix 13 Fix10. EMBOSS-4.0.0/doc/programs/html/banana.1.banana.gif EMBOSS-4.0.0/doc/programs/html/tcode.2.tcode.gif 14 Aug 2006: These graphics example outputs were missing from the distribution. When you run make install they will be copied to the installed documentation. Fix 11. EMBOSS-4.0.0/emboss/merger.c EMBOSS-4.0.0/emboss/needle.c EMBOSS-4.0.0/emboss/prophet.c EMBOSS-4.0.0/emboss/water.c 14 Aug 2006: These programs calculate an internal path size from the lengths of the input sequences. For sequences that are too long, a fatal error is produced. But if the sequences are extremely long, the test failed and the program gave a segmentation fault. This fix tests in a different way that will catch all cases. Fix 12. See Fix13 Fix 13. EMBOSS-4.0.0/ajax/ajacd.c EMBOSS-4.0.0/ajax/ajfeat.c EMBOSS-4.0.0/ajax/ajfeat.h EMBOSS-4.0.0/ajax/ajreport.c EMBOSS-4.0.0/ajax/ajreport.h EMBOSS-4.0.0/emboss/fuzznuc.c EMBOSS-4.0.0/emboss/fuzzpro.c EMBOSS-4.0.0/emboss/fuzztran.c 21 Aug 2006: This provides new qualifiers to limit report output to a number of hits in total (-rmaxall) or for any one sequence (-rmaxseq). It also fixes reversed feature locations for reports in EMBL format. The files fixed overlap with earlier fixes which are included here. 09 Aug 2006: Fix 8: In release 4.0.0 these 3 programs were changed to report even when no hits were found. The aim was to avoid empty output for a single sequence. Many users were running these programs over large input sets, and now get excessively large output files. The change has been reversed. Fix 9 makes sure a small output file is produced when no hits are found. 09 Aug 2006: Fix 9: When closing a report (with ajReportClose) make sure a standard report header and footer are printed if nothing has been reported so far. The header reports the command line. The new footer reports the total number of sequences and features reported. Reversed sequence positions are corrected for listfile report format. No header can be reported for some formats (EMBL, Genbank, GFF, PIR, Swiss, Excel, Feattable). 14 Aug 2006: Fix12: This fixes a bug where putting -ofopenfile on the command line for features output failed to set the feature output format. Fix 14. EMBOSS-4.0.0/ajax/ajseqread.c EMBOSS-4.0.0/ajax/ajseqread.h EMBOSS-4.0.0/ajax/ajseqwrite.c EMBOSS-4.0.0/emboss/dbiblast.c EMBOSS-4.0.0/emboss/dbifasta.c EMBOSS-4.0.0/emboss/dbxfasta.c EMBOSS-4.0.0/emboss/acd/dbiblast.acd EMBOSS-4.0.0/emboss/acd/dbifasta.acd EMBOSS-4.0.0/emboss/acd/dbxfasta.acd 24 Aug 2006: Pearson format preserves dbname:entryname style IDs NCBI format parsing (includes FASTA format parsing) extracts database name from NCBI piped ids and uses on output unless EMBOSS has defined some other database name. Three indexing programs call the NCBI parsing function which has an extra argument. Fasta parsing was also modified to allow UniProt style (yet another FASTA format) where the accession number is in brackets. The "idacc" default format now removes brackets before checking for an accession number or version next on the line. From golharam at umdnj.edu Fri Aug 25 11:25:30 2006 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 25 Aug 2006 11:25:30 -0400 Subject: [EMBOSS] Installation problems of EMBOSS explorer In-Reply-To: <4f3a50530608242048u7f978211se5df35673cd5a20e@mail.gmail.com> Message-ID: <006101c6c85a$b39f6f20$2f01a8c0@GOLHARMOBILE1> It looks like you need to install other perl modules includes Mail::Send, and Parse::RecDescent. If you don't have root permission to install, then you can install in a local directory. I *think* the command is 'make DESTDIR=/home/sea/perl5.8.5 install' where DESTDIR is the variable to indicate the installation root. Ryan -----Original Message----- From: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Sea Sent: Thursday, August 24, 2006 11:49 PM To: emboss at lists.open-bio.org Subject: Re: [EMBOSS] Installation problems of EMBOSS explorer Hi Ryan, Here is the error shown: server: emboss [source/emboss-explorer]> ./install installing EMBOSS Explorer perl modules... Warning: prerequisite Mail::Send failed to load: Can't locate Mail/Send.pm in @INC (@INC contains: /usr/perl5/5.6.1/lib/sun4-solaris-64int /usr/perl5/5.6.1/lib /usr/perl5/site_perl/5.6.1/sun4-solaris-64int /usr/perl5/site_perl/5.6.1 /usr/perl5/site_perl /usr/perl5/vendor_perl/5.6.1/sun4-solaris-64int /usr/perl5/vendor_perl/5.6.1 /usr/perl5/vendor_perl .) at (eval 4) line 3. Warning: prerequisite Parse::RecDescent failed to load: Can't locate Parse/RecDescent.pm in @INC (@INC contains: /usr/perl5/5.6.1/lib/sun4-solaris-64int /usr/perl5/5.6.1/lib /usr/perl5/site_perl/5.6.1/sun4-solaris-64int /usr/perl5/site_perl/5.6.1 /usr/perl5/site_perl /usr/perl5/vendor_perl/5.6.1/sun4-solaris-64int /usr/perl5/vendor_perl/5.6.1 /usr/perl5/vendor_perl .) at (eval 5) line 3. 'PREREQ_FATAL' is not a known MakeMaker parameter name. Writing Makefile for EMBOSS::GUI Manifying blib/man3/EMBOSS::GUI.3 Manifying blib/man3/EMBOSS::GUI::XHTML.3 Manifying blib/man3/EMBOSS::GUI::Conf.3 Manifying blib/man3/EMBOSS::ACD.3 Manifying blib/man3/EMBOSS::GUI.3 Warning: You do not have permissions to install into /usr/perl5/site_perl/5.6.1/sun4-solaris-64int at /usr/perl5/5.6.1/lib/ExtUtils/Install.pm line 85. mkdir /usr/perl5/site_perl/5.6.1/EMBOSS: Permission denied at /usr/perl5/5.6.1/lib/ExtUtils/Install.pm line 138 *** Error code 255 make: Fatal error: Command failed for target `pure_site_install' I guess that I don't have a root privilege so can't access the /usr/perl5 directory. Thus I installed perl 5.8.5 in my folder and then modified the emboss-explorer "Makefile", but still failed. Hope any experienced friends give me some suggestions. :-) Thank you! On 8/23/06, Ryan Golhar wrote: > What are the errors you are getting? > > -----Original Message----- > From: emboss-bounces at lists.open-bio.org > [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Sea > Sent: Wednesday, August 23, 2006 9:01 AM > To: emboss at lists.open-bio.org > Subject: [EMBOSS] Installation problems of EMBOSS explorer > > > Hi, > > This is my first time to install EMBOSS explorer, > but I couldn't install successfully. > > It showed some error messages and seem problems about the perl module. > > Because I used a non-root-privilege account to do the thing and > installed a non-default directory, I'm not sure whether it caused that > results. > > Would any experienced friends tell me some hints? > > Thanks a lot! :-) > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss _______________________________________________ EMBOSS mailing list EMBOSS at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss From mthon at tamu.edu Fri Aug 25 17:31:41 2006 From: mthon at tamu.edu (Michael Thon) Date: Fri, 25 Aug 2006 16:31:41 -0500 Subject: [EMBOSS] EMBOSS 4.0.0 Latest Fixes In-Reply-To: <44EF0256.1040802@ebi.ac.uk> References: <44EF0256.1040802@ebi.ac.uk> Message-ID: <005A5F53-7C8E-49CB-9AEA-B34C13053B0A@tamu.edu> Hi Peter - Will you be releasing an update to the emboss distribution that includes these changes? cheers Mike On Aug 25, 2006, at 8:59 AM, Peter Rice wrote: > I have posted some further fixes on the EMBOSS FTP site. None are > critical. Users have been reporting interesting bugs. Some were > also in > release 3.0.0. > > The fuzznuc, fuzzpro and fuzztran reports were changed in 4.0.0 to > always report something. Unfortunately users running searches over the > whole database found their output files were very large. We have > changed > the way reports work as follows: > > 1. fuzznuc, fuzzpro and fuzztran again report only sequences with hits > > 2. when a report is closed, a default header and footer are written > (solving the problem of empty output files) > > 3. for sites that had concerns about searches for trivial patterns > taking too long and generating too much output, reports have 2 new > associated qualifiers. -rmaxall limits the total number of matches > reported (fuzznuc, fuzzpro and fuzztran terminate when the limit is > reached), -rmaxseq limits the maximum number of hits for one sequence. > > We also have various fixes for reporting matches on the reverse > strand, > and for improved parsing of FASTA file IDs. > > To update your EMBOSS 4.0.0 release, go to: > > ftp://emboss.open-bio.org/pub/EMBOSS/fixes/ > > File README.fixes (see below) lists the files and describes the fixes. > > Copy the files to the indicated directories and reinstall. > > regards, > > Peter Rice > > file README.fixes 25-aug-2006 > > The files in this directory are bugfix replacements for files in > the EMBOSS-4.0.0 distribution. Just drop the replacement files in > the location shown and redo the 'make install.' > > > Fix 1. EMBOSS-4.0.0/nucleus/embpatlist.c > > 31 Jul 2006: Fixes a problem with searching for patterns and regular > expression in the reverse strand of nucleotide sequences. The change > is to use ajSeqReverseForce (always reverses the sequence provided) > instead of ajSeqReverseDo (which only reverses if the reverse flag is > set) > > 9 Aug 2006: Revised to also fix a problem with reverse strand sequence > positions. > > > Fix 2. EMBOSS-4.0.0/ajax/ajfile.c > > 31 Jul 2006: This fixes a bug where deleting the last line of buffered > input fails to reset the pointer to the last buffered line. This only > affected debug traces. Unfortunately, the ajFileBuffClear function > does call the debug trace. In practice we have only seen this bug when > processing sequence data in EMBL format from an MRS server. > > Fix 3. EMBOSS-4.0.0/ajax/ajnam.c > > 31 Jul 3006: New database access methods MRS and DBFETCH need to be > explicitly turned on so that showdb can report them. > > > Fix 4. EMBOSS-4.0.0/ajax/ajseqdb.c > > 31 Jul 2006: The new MRS access method used a general search. This > gave strange results when the ID or accession appeared in any other > entry. It appears that MRS can search for id or accession only. This > worked on the main MRS server at least. > > MRS access will be further extended in the next release. Please > contact the developers emboss-bug at emboss.open-bio.org if you would > like to help test new features in MRS access. > > 25 Aug 2006: Further change to allow multiple %s replacements in > complex URLs for access method URL. Needed for complex SRS queries to > resolve EMBL IDs so the following definition can be used for EMBL > (warning, the URL may wrap badly in this email!) > > DB embl [ > method: "url" > format: "embl" > type: "N" > url: > > "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-noSession+-ascii+-vn+2+- > e+[embl-id:%s]|[embl-acc:%s]|([emblidacc-id:%s]>embl)" > comment: "EMBL from SRS including old IDs" > ] > > Fix 5. EMBOSS-4.0.0/configure > > 07 Aug 2006: Fix configuration problem on Intel Mac machines. Make > sure > this file is executable (chmod 755 configure) after downloading it. > > Fix 6. EMBOSS-4.0.0/ajax/ajseq.c > > 09 Aug 2006: Return correct USA for "asis::" sequence input. > > Fix 7. EMBOSS-4.0.0/emboss/dreg.c > > 09 Aug 2006: Correct sequence positions on the reverse strand. > > Fix 8. See Fix 13 > > Fix 9. See Fix 13 > > Fix10. EMBOSS-4.0.0/doc/programs/html/banana.1.banana.gif > EMBOSS-4.0.0/doc/programs/html/tcode.2.tcode.gif > > 14 Aug 2006: These graphics example outputs were missing from the > distribution. When you run make install they will be copied to the > installed documentation. > > Fix 11. EMBOSS-4.0.0/emboss/merger.c > EMBOSS-4.0.0/emboss/needle.c > EMBOSS-4.0.0/emboss/prophet.c > EMBOSS-4.0.0/emboss/water.c > > 14 Aug 2006: These programs calculate an internal path size from the > lengths of the input sequences. For sequences that are too long, a > fatal error is produced. But if the sequences are extremely long, the > test failed and the program gave a segmentation fault. This fix tests > in a different way that will catch all cases. > > Fix 12. See Fix13 > > Fix 13. EMBOSS-4.0.0/ajax/ajacd.c > EMBOSS-4.0.0/ajax/ajfeat.c > EMBOSS-4.0.0/ajax/ajfeat.h > EMBOSS-4.0.0/ajax/ajreport.c > EMBOSS-4.0.0/ajax/ajreport.h > EMBOSS-4.0.0/emboss/fuzznuc.c > EMBOSS-4.0.0/emboss/fuzzpro.c > EMBOSS-4.0.0/emboss/fuzztran.c > > 21 Aug 2006: This provides new qualifiers to limit report output to a > number of hits in total (-rmaxall) or for any one sequence > (-rmaxseq). It also fixes reversed feature locations for reports in > EMBL format. The files fixed overlap with earlier fixes which are > included here. > > 09 Aug 2006: Fix 8: In release 4.0.0 these 3 programs were changed > to report > even when no hits were found. The aim was to avoid empty output for a > single sequence. > > Many users were running these programs over large input sets, and now > get excessively large output files. > > The change has been reversed. Fix 9 makes sure a small output > file is produced when no hits are found. > > 09 Aug 2006: Fix 9: When closing a report (with ajReportClose) make > sure a > standard report header and footer are printed if nothing has been > reported so far. The header reports the command line. The new footer > reports the total number of sequences and features reported. > > Reversed sequence positions are corrected for listfile report format. > > No header can be reported for some formats (EMBL, Genbank, GFF, PIR, > Swiss, Excel, Feattable). > > 14 Aug 2006: Fix12: This fixes a bug where putting -ofopenfile on the > command > line for features output failed to set the feature output format. > > > Fix 14. EMBOSS-4.0.0/ajax/ajseqread.c > EMBOSS-4.0.0/ajax/ajseqread.h > EMBOSS-4.0.0/ajax/ajseqwrite.c > EMBOSS-4.0.0/emboss/dbiblast.c > EMBOSS-4.0.0/emboss/dbifasta.c > EMBOSS-4.0.0/emboss/dbxfasta.c > EMBOSS-4.0.0/emboss/acd/dbiblast.acd > EMBOSS-4.0.0/emboss/acd/dbifasta.acd > EMBOSS-4.0.0/emboss/acd/dbxfasta.acd > > 24 Aug 2006: Pearson format preserves dbname:entryname style IDs > NCBI format parsing (includes FASTA format parsing) extracts database > name from NCBI piped ids and uses on output unless EMBOSS has defined > some other database name. > > Three indexing programs call the NCBI parsing function which has an > extra argument. > > Fasta parsing was also modified to allow UniProt style (yet another > FASTA format) where the accession number is in brackets. The "idacc" > default format now removes brackets before checking for an accession > number or version next on the line. > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From kvddrift at earthlink.net Sat Aug 26 11:05:58 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sat, 26 Aug 2006 11:05:58 -0400 Subject: [EMBOSS] EMBOSS 4.0.0 Latest Fixes In-Reply-To: <44EF0256.1040802@ebi.ac.uk> References: <44EF0256.1040802@ebi.ac.uk> Message-ID: <989F3713-DB05-45C9-9F3D-4CC9D36E4AB4@earthlink.net> On Aug 25, 2006, at 9:59 AM, Peter Rice wrote: > EMBOSS-4.0.0/emboss/acd/dbiblast.acd FYI, this file is not in the fixes directory. Also the file restrict.c is in the fixes directory, but not in the readme. - Koen. From ajb at ebi.ac.uk Sun Aug 27 04:50:11 2006 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Sun, 27 Aug 2006 09:50:11 +0100 (BST) Subject: [EMBOSS] EMBOSS 4.0.0 Latest Fixes In-Reply-To: <989F3713-DB05-45C9-9F3D-4CC9D36E4AB4@earthlink.net> References: <44EF0256.1040802@ebi.ac.uk> <989F3713-DB05-45C9-9F3D-4CC9D36E4AB4@earthlink.net> Message-ID: <55707.81.98.244.247.1156668611.squirrel@webmail.ebi.ac.uk> >> EMBOSS-4.0.0/emboss/acd/dbiblast.acd > > FYI, this file is not in the fixes directory. And, according to CVS, it shouldn't be. I've removed it from the README.fixes file. > Also the file > restrict.c is in the fixes directory, but not in the readme. This concerned the reporting of complementary strand matches in EMBL feature tables. I've appended a note to the README.fixes file. Thanks Alan From ajb at ebi.ac.uk Sun Aug 27 06:32:51 2006 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Sun, 27 Aug 2006 11:32:51 +0100 (BST) Subject: [EMBOSS] EMBOSS 4.0.0 Latest Fixes In-Reply-To: <005A5F53-7C8E-49CB-9AEA-B34C13053B0A@tamu.edu> References: <44EF0256.1040802@ebi.ac.uk> <005A5F53-7C8E-49CB-9AEA-B34C13053B0A@tamu.edu> Message-ID: <50816.81.98.244.247.1156674771.squirrel@webmail.ebi.ac.uk> Dear Michael, > Hi Peter I'll have to do in his absence. :-) > Will you be releasing an update to the emboss distribution > that includes these changes? We're keeping that under review. For now I've put a UNIX 'patch' file on the anonymous ftp server which may make things easier for people. See my next posting. ATB Alan From ajb at ebi.ac.uk Sun Aug 27 06:47:07 2006 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Sun, 27 Aug 2006 11:47:07 +0100 (BST) Subject: [EMBOSS] Updating EMBOSS: patch files Message-ID: <51319.81.98.244.247.1156675627.squirrel@webmail.ebi.ac.uk> As the start of an experimental service, discussed at an EMBOSS developers' meeting, I've created a 'patches' directory on the anonymous ftp server: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/ The purpose of this directory is to provide UNIX 'patch' (context diff) files. These should make EMBOSS easier to update between releases as you only need to apply one patch rather than all the individual fixes from the directory above. This depends on your system having the 'patch' command installed. As it is an experimental service there may be the odd dragon lurking. Let us know if you find one. I append the README.patch file from the above directory which explains how to use the patch files. Alan The file(s) in this directory are standard UNIX 'patch' files and can be used to update the base EMBOSS release with all the fixes given in: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README.fixes The filenames are of the format 'patch-1-X.gz' where 'X' represents the last fix incorporated: so a file called patch-1-10.gz will incorporate fixes from Fix 1 to Fix 10 as given in the README.fixes file. To update the base EMBOSS installation (where x.y.z is the version): 1. Download a fresh EMBOSS-x.y.z.tar.gz and unpack it with gunzip and tar. 2. Download the required patch file. 3. cd EMBOSS-x.y.z 4. gunzip -c /somewhere/patch-1-X.gz | patch -p1 or 1-3 as above 4. gunzip /somewhere/patch-1-X.gz patch -p1 < /somewhere/patch-1-X Then configure EMBOSS as normal. N.B. (27th Aug 2006): This is a new method for providing updates and therefore not tested in anger by the community. Please let us know of any problems. From jgkannan at rediffmail.com Tue Aug 29 03:04:46 2006 From: jgkannan at rediffmail.com (J.G.Kannan) Date: 29 Aug 2006 07:04:46 -0000 Subject: [EMBOSS] Few Queries Message-ID: <20060829070446.14707.qmail@webmail32.rediffmail.com> Hi All, I am newbie to this application. I have few queries mentioned below. It would be great if anyone send me the answers, 1. Dose this application supports parallel computing? 2. EMBOSS supports S10x86 (32 and 64 bit) ? 3. What are programming standards and technology your using? Thanks in advance -J.G.Kannan From shrish at ccmb.res.in Tue Aug 29 07:37:46 2006 From: shrish at ccmb.res.in (Shrish Tiwari) Date: Tue, 29 Aug 2006 18:07:46 +0630 Subject: [EMBOSS] (no subject) Message-ID: Hi! Is there a program in EMBOSS to extract the coordinates of exons? Shrish ______________________________________________________________________ Dr. Shrish Tiwari, Scientist BIC, Centre for Cellular and Molecular Biology Uppal Road, Hyderabad - 500 007 Phone: 91-40-7192776 (work), 91-40-7156603 (home) email: shrish at ccmb.res.in ______________________________________________________________________ From David.Bauer at schering.de Tue Aug 29 09:29:10 2006 From: David.Bauer at schering.de (David.Bauer at schering.de) Date: Tue, 29 Aug 2006 15:29:10 +0200 Subject: [EMBOSS] Antwort: (no subject) In-Reply-To: Message-ID: Hi, you can use 'showfeat' with the option '-pos' to display sequence features with the positions. If your exons are annotated as 'mRNA' in the feature table you could use: showfeat -pos -matchtype mRNA To get only the positions without the ascii graphics use '-width 0' HTH, David. emboss-bounces at lists.open-bio.org schrieb am 29/08/2006 13:37:46: > Hi! > > Is there a program in EMBOSS to extract the coordinates of exons? > > Shrish > > > ______________________________________________________________________ > Dr. Shrish Tiwari, Scientist > BIC, Centre for Cellular and Molecular Biology > Uppal Road, Hyderabad - 500 007 > Phone: 91-40-7192776 (work), 91-40-7156603 (home) > email: shrish at ccmb.res.in > ______________________________________________________________________ > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From simon.andrews at bbsrc.ac.uk Thu Aug 31 06:48:56 2006 From: simon.andrews at bbsrc.ac.uk (Simon Andrews) Date: Thu, 31 Aug 2006 11:48:56 +0100 Subject: [EMBOSS] (no subject) In-Reply-To: References: Message-ID: <8E95A140-DDA1-46C0-9990-5979068E3E57@bbsrc.ac.uk> On 29 Aug 2006, at 12:37, Shrish Tiwari wrote: > Hi! > > Is there a program in EMBOSS to extract the coordinates of exons? It depends what you mean. If you want to extract the transcript sequence from a genomic sequence with an mRNA feature defined in its header then you can use coderet. If you want to figure out where the exon positions are in a sequence and you have an mRNA and a genomic sequence then you can use est2genome. If you just want to view the header annotation then entret will give you that. Simon. From tao.song at calibrant.com Thu Aug 31 11:01:38 2006 From: tao.song at calibrant.com (Tao Song) Date: Thu, 31 Aug 2006 15:01:38 -0000 Subject: [EMBOSS] How to modify a program? References: Message-ID: <001a01c654d4$6bfc13c0$1b02a8c0@tao> Hi, I am new to Unix system, so sorry if it is a too simple question. I need to modify the DIGEST program (\EMBOSS-4.0.0\emboss\digest) to change some rules for trypsin digestion. The part of the program that I need to modify is in another program (EMBOSS-4.0.0\nucleus\embprop.c). After modify the embprop program I compiled with gcc and got a embprop.o file. But when I ran the DIGEST program it still give the same results and didn't change. Are there some steps that I missed? Thanks a lot for your help! Regards, Tao From sbassi at gmail.com Thu Aug 31 11:25:03 2006 From: sbassi at gmail.com (Sebastian Bassi) Date: Thu, 31 Aug 2006 12:25:03 -0300 Subject: [EMBOSS] How to modify a program? In-Reply-To: <001a01c654d4$6bfc13c0$1b02a8c0@tao> References: <001a01c654d4$6bfc13c0$1b02a8c0@tao> Message-ID: On 3/31/06, Tao Song wrote: > change. Are there some steps that I missed? What I did once was to do a new configure and make, that compiled only the changed file (don't ask me how the compiler knew that I changed only one .c file). Also check for path problems (maybe you are executing a version that is in the path before the one you want to run) -- Bioinformatics news: http://www.bioinformatica.info Lriser: http://www.linspire.com/lraiser_success.php?serial=318 From golharam at umdnj.edu Thu Aug 31 14:38:50 2006 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 31 Aug 2006 14:38:50 -0400 Subject: [EMBOSS] Building EMBOSS error Message-ID: <025e01c6cd2c$b564b910$2f01a8c0@GOLHARMOBILE1> Hi, I'm building EMBOSS 4.0.0 (with patch 1-15) on Solaris uname -a: SunOS siriusC 5.8 Generic_117350-38 sun4u sparc SUNW,Sun-Fire When I run the configure script I get: checking for purify... no expr: syntax error ./configure: test: =: unary operator expected checking if any threading type is given... No I'm still able to build fine but wasn't sure if this error might cause some problems... Ryan From ajb at ebi.ac.uk Thu Aug 31 16:18:11 2006 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Thu, 31 Aug 2006 21:18:11 +0100 (BST) Subject: [EMBOSS] Building EMBOSS error In-Reply-To: <025e01c6cd2c$b564b910$2f01a8c0@GOLHARMOBILE1> References: <025e01c6cd2c$b564b910$2f01a8c0@GOLHARMOBILE1> Message-ID: <1089.81.131.22.33.1157055491.squirrel@webmail.ebi.ac.uk> > When I run the configure script I get: > > checking for purify... no > expr: syntax error > ./configure: test: =: unary operator expected > checking if any threading type is given... No > > I'm still able to build fine but wasn't sure if this error might cause > some problems... That is a message which can be safely ignored. I do need to tidy that up though - thanks for the reminder. Alan From lasergene at gmail.com Tue Aug 8 03:10:05 2006 From: lasergene at gmail.com (Kevin Hwang) Date: Tue, 8 Aug 2006 11:10:05 +0800 Subject: [EMBOSS] EMBOSS Digest, Vol 13, Issue 4 In-Reply-To: References: Message-ID: <3d6c72510608072010h63a8b123p8d3e86e6da1fef72@mail.gmail.com> Hi, Everyone, I am learning EMBOSSwin(2.10.0-win-0.8) by myself recently. But a problem puzzled me when I want to align mutiple sequences. I used the command "emma", it can't work. I don't know why and how to resolve it. Does anyone help me? many thanks. Kevin Hwang. From ajb at ebi.ac.uk Tue Aug 8 10:00:59 2006 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Tue, 8 Aug 2006 11:00:59 +0100 (BST) Subject: [EMBOSS] Antwort: Re: EMBOSS Digest, Vol 13, Issue 4 In-Reply-To: References: <3d6c72510608072010h63a8b123p8d3e86e6da1fef72@mail.gmail.com> Message-ID: <43156.81.98.244.247.1155031259.squirrel@webmail.ebi.ac.uk> Hello David, > 2) > Unfortunately this won't help much, because there seems to be a problem > with emma also in the new windows version. I can't reproduce the problem. > emma is not a full application, but only an interface to the multiple > alignment program clustalW. > The current windows version of EMBOSS contains an clustalw executable, but > this doesn't work. (Error message I get: "The system cannot execute the > specified program"). Well that's definitely a Microsoft error message rather than an EMBOSS one. I have tried the clustalw.exe supplied with EMBOSS-MS on a few Windows setups on a range of machines just now. None showed that error. Admittedly some of the machines required the vcredist_x86.exe Visual C/C++ 2005 runtime libraries added but that was mentioned in the announcement (and I've just put a README.win on the ftp server saying the same). Besides, that would usually give a "Missing DLL" error, not the "Cannot Execute" one. I do find it odd that clustalw.exe gives that error but the emboss applications do not: they were all built using the same compiler on the same machine. DependencyWalker (http://www.dependencywalker.com) shows that the required modules on XP for clustalw are kernel32.dll, msvcr80.dll, msvcrt.dll and ntdll.dll. You could try installing Dependencywalker and seeing whether it detects any missing modules for clustalw on your system. Does the problem occur on your home XP installations, your Schering installation or both? > I replaced it with the XP executable from > ftp://ftp.ebi.ac.uk/pub/software/dos/clustalw/ but now I'm getting a > different problem. > The clustalw used directly runs without problem. But if called from emma > it complains: > CLUSTAL W (1.83) Multiple Sequence Alignments > Error: unknown option /-infile=00002432A > Error: Failed to open filename '00002432B' > Problem writing out EMBOSS alignment file > clustalw needs just /infile= and not /-infile= Yes, it would do that :-) Versions of clustalw for Windows found on the network usually do not have the UNIX-style command line. You must use the clustalw.exe supplied with EMBOSS-MS which does have the UNIX command line. > Btw. I could not reproduce the Path overwriting on any generic XP (Pro or > Home) so it has something to do with our local XP installtion but I could > not find the reason so far. I'm still intrigued by that one. I expect that you've checked that there isn't another program called setenv.exe on the system? ATB Alan From David.Bauer at SCHERING.DE Tue Aug 8 06:19:00 2006 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Tue, 8 Aug 2006 08:19:00 +0200 Subject: [EMBOSS] Antwort: Re: EMBOSS Digest, Vol 13, Issue 4 In-Reply-To: <3d6c72510608072010h63a8b123p8d3e86e6da1fef72@mail.gmail.com> Message-ID: Hi, 1) If you just start with emboss on windows, why don't you try the latest version 4.0.0 ? You can find it in ftp://emboss.open-bio.org/pub/EMBOSS/windows/. 2) Unfortunately this won't help much, because there seems to be a problem with emma also in the new windows version. emma is not a full application, but only an interface to the multiple alignment program clustalW. The current windows version of EMBOSS contains an clustalw executable, but this doesn't work. (Error message I get: "The system cannot execute the specified program"). I replaced it with the XP executable from ftp://ftp.ebi.ac.uk/pub/software/dos/clustalw/ but now I'm getting a different problem. The clustalw used directly runs without problem. But if called from emma it complains: CLUSTAL W (1.83) Multiple Sequence Alignments Error: unknown option /-infile=00002432A Error: Failed to open filename '00002432B' Problem writing out EMBOSS alignment file clustalw needs just /infile= and not /-infile= So I guess Alan can resolve what's going on here ;-) Ciao, David. Btw. I could not reproduce the Path overwriting on any generic XP (Pro or Home) so it has something to do with our local XP installtion but I could not find the reason so far. emboss-bounces at lists.open-bio.org schrieb am 08/08/2006 05:10:05: > Hi, Everyone, > I am learning EMBOSSwin(2.10.0-win-0.8) by myself recently. But a problem > puzzled me when I want to align mutiple sequences. I used the command > "emma", it can't work. I don't know why and how to resolve it. Does anyone > help me? many thanks. > > Kevin Hwang. > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From ajb at ebi.ac.uk Tue Aug 8 12:36:31 2006 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Tue, 8 Aug 2006 13:36:31 +0100 (BST) Subject: [EMBOSS] Antwort: Re: EMBOSS Digest, Vol 13, Issue 4 In-Reply-To: References: <43156.81.98.244.247.1155031259.squirrel@webmail.ebi.ac.uk> Message-ID: <52915.81.98.244.247.1155040591.squirrel@webmail.ebi.ac.uk> Hello David, > It was the missing msvcr80.dll. I have the older version msvcr70.dll. > The only idea I have why there was no "dll not found" error is, that > windows tries > to fix the missing dll by falling back to the older version and clustalw > then > runs into trouble ? That is good to know. Thanks. The installer does have the capability of safely (it says) adding system DLLs to the Windows system directory but I'm a little wary of doing that at the moment. There dragons may live. For the alpha test, at least, it is probably better that people install vcredist_x86.exe as necessary. Thanks for the Path info. Curious indeed. Alan From David.Bauer at SCHERING.DE Tue Aug 8 11:57:48 2006 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Tue, 8 Aug 2006 13:57:48 +0200 Subject: [EMBOSS] Antwort: Re: EMBOSS Digest, Vol 13, Issue 4 In-Reply-To: <43156.81.98.244.247.1155031259.squirrel@webmail.ebi.ac.uk> Message-ID: Hello Alan, > DependencyWalker (http://www.dependencywalker.com) shows that the That's a nice tool ! > required modules on XP for clustalw are kernel32.dll, msvcr80.dll, > msvcrt.dll and ntdll.dll. You could try installing Dependencywalker > and seeing whether it detects any missing modules for clustalw on > your system. It was the missing msvcr80.dll. I have the older version msvcr70.dll. The only idea I have why there was no "dll not found" error is, that windows tries to fix the missing dll by falling back to the older version and clustalw then runs into trouble ? > > Btw. I could not reproduce the Path overwriting on any generic XP (Pro or > > Home) so it has something to do with our local XP installtion but I could > > not find the reason so far. > > I'm still intrigued by that one. I expect that you've checked that > there isn't another program called setenv.exe on the system? The only special thing is, that I have a Path under user variables AND under system variables. But I tried to reproduce this situation on another machine and the emboss dir was correctly appended there to the system Path. Curious. Thanks, David. From hrh at sanger.ac.uk Fri Aug 11 12:54:09 2006 From: hrh at sanger.ac.uk (Hans Rudolf Hotz) Date: Fri, 11 Aug 2006 13:54:09 +0100 (BST) Subject: [EMBOSS] display of long ensembl and vega identifiers in alignments In-Reply-To: References: Message-ID: Hi ensembl and vega identifiers are very long, and are therefore cut when used in alignment programs like matcher, eg: cbi1b[hrh]59: matcher pep1 pep2 stdout Finds the best local alignments between two sequences ######################################## # Program: matcher # Rundate: Fri Aug 11 2006 13:45:51 # Align_format: markx0 # Report_file: stdout ######################################## #======================================= # # Aligned_sequences: 2 # 1: OTTHUMT00000072262 # 2: ENST00000216277 # Matrix: EBLOSUM62 # Gap_penalty: 14 # Extend_penalty: 4 # # Length: 745 # Identity: 745/745 (100.0%) # Similarity: 745/745 (100.0%) # Gaps: 0/745 ( 0.0%) # Score: 3818 # # #======================================= 10 20 30 40 50 OTTHUM MPFPVTTQGSQQTQPPQKHYGITSPISLAAPKETDCVLTQKLIETLKPFG :::::::::::::::::::::::::::::::::::::::::::::::::: ENST00 MPFPVTTQGSQQTQPPQKHYGITSPISLAAPKETDCVLTQKLIETLKPFG 10 20 30 40 50 A few months back, I played arround with the source code and changed one of the library files (ajalign.c). This now allows the display of up to 20 characters, by using a new output format "pairln" for sequence alignment programs, like matcher or needle. This is in comparison to the default which displays only the first 6 characters, or "pair" which displays the first 13 characters, eg: cbi1b[hrh]65: matcher pep1 pep2 stdout -aformat pairln Finds the best local alignments between two sequences ######################################## # Program: matcher # Rundate: Fri Aug 11 2006 13:49:41 # Align_format: pairln # Report_file: stdout ######################################## #======================================= # # Aligned_sequences: 2 # 1: OTTHUMT00000072262 # 2: ENST00000216277 # Matrix: EBLOSUM62 # Gap_penalty: 14 # Extend_penalty: 4 # # Length: 745 # Identity: 745/745 (100.0%) # Similarity: 745/745 (100.0%) # Gaps: 0/745 ( 0.0%) # Score: 3818 # # #======================================= OTTHUMT00000072262 1 MPFPVTTQGSQQTQPPQKHYGITSPISLAAPKETDCVLTQKLIETLKPFG 50 |||||||||||||||||||||||||||||||||||||||||||||||||| ENST00000216277 1 MPFPVTTQGSQQTQPPQKHYGITSPISLAAPKETDCVLTQKLIETLKPFG 50 Any chance something like this could make it into the distributed code? Thanks, Hans From pmr at ebi.ac.uk Fri Aug 11 13:53:23 2006 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 11 Aug 2006 14:53:23 +0100 Subject: [EMBOSS] display of long ensembl and vega identifiers in alignments In-Reply-To: References: Message-ID: <44DC8BD3.6080800@ebi.ac.uk> Hans Rudolf Hotz wrote: > A few months back, I played arround with the source code and changed one > of the library files (ajalign.c). This now allows the display of up to 20 > characters, by using a new output format "pairln" for sequence alignment > programs, like matcher or needle. This is in comparison to the default > which displays only the first 6 characters, or "pair" which displays the > first 13 characters, eg: We can make the ID arbitrarily long for a "new" alignment format. We will need formats similar to the existing matcher and needle outputs to avoid breaking too many existing parsers (I remember when NCBI changed the use of a blank at the start of each line of blast output and almost all parsers had to change). The formats are easy to make (as you found out) from the existing ones. We need to decide what to do with the standard alignment formats that have 6 characters in their definition (I assume this goes back to the days of PIR database identifiers when FASTP was first written). As we cannot fit many of the existing identifiers, we can make up unique identifiers for these (truncate the identifier, and make the names unique if they match). Or, should we change the existing formats to allow longer IDs? What do the authors of parsers think? regards, Peter From golharam at umdnj.edu Fri Aug 11 17:51:23 2006 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 11 Aug 2006 13:51:23 -0400 Subject: [EMBOSS] 404 error on web site Message-ID: <007a01c6bd6e$c29cb560$2f01a8c0@GOLHARMOBILE1> I'm viewing http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/index.html. I click on the "EMBASSY applications" link and I get a 404 error. From golharam at umdnj.edu Fri Aug 11 19:47:46 2006 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 11 Aug 2006 15:47:46 -0400 Subject: [EMBOSS] Compiling EMNU fails with EMBOSS 4.0.0 Message-ID: <008201c6bd7f$04ac6120$2f01a8c0@GOLHARMOBILE1> So I'm recompiling the EMNU package to link with EMBOSS 4.0.0 and I'm getting some compiler errors that I don't get with EMBOSS 3.0.0: emnu.c: In function `populate_program_menus': emnu.c:1307: `GPnode' undeclared (first use in this function) emnu.c:1307: (Each undeclared identifier is reported only once emnu.c:1307: for each function it appears in.) emnu.c:1307: syntax error before "gl" emnu.c:1314: `gl' undeclared (first use in this function) emnu.c:1315: warning: `ajStrLen' is deprecated (declared at /usr/include/ajstr.h:591) emnu.c:1315: warning: `ajStrLen' is deprecated (declared at /usr/include/ajstr.h:591) emnu.c:1322: warning: `ajStrLen' is deprecated (declared at /usr/include/ajstr.h:591) emnu.c:1324: warning: `ajStrLen' is deprecated (declared at /usr/include/ajstr.h:591) emnu.c:1325: warning: `ajStrStr' is deprecated (declared at /usr/include/ajstr.h:644) emnu.c:1327: warning: `ajStrStr' is deprecated (declared at /usr/include/ajstr.h:644) emnu.c:1330: warning: `ajStrStr' is deprecated (declared at /usr/include/ajstr.h:644) emnu.c:1330: warning: `ajStrStr' is deprecated (declared at /usr/include/ajstr.h:644) emnu.c: In function `populate_menu': emnu.c:1356: `GPnode' undeclared (first use in this function) emnu.c:1356: syntax error before "gl" emnu.c:1373: `gl' undeclared (first use in this function) emnu.c:1384: warning: `ajStrStr' is deprecated (declared at /usr/include/ajstr.h:644) emnu.c:1422: warning: `ajStrAssC' is deprecated (declared at /usr/include/ajstr.h:538) emnu.c:1424: too few arguments to function `embGrpKeySearchProgs' make[1]: *** [emnu.o] Error 1 make[1]: Leaving directory `/usr/src/redhat/BUILD/EMNU-1.05/source' make: *** [all-recursive] Error 1 Is anyone else able to compile EMNU using EMBOSS 4? Ryan From ajb at ebi.ac.uk Fri Aug 11 21:59:00 2006 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Fri, 11 Aug 2006 22:59:00 +0100 (BST) Subject: [EMBOSS] Compiling EMNU fails with EMBOSS 4.0.0 In-Reply-To: <008201c6bd7f$04ac6120$2f01a8c0@GOLHARMOBILE1> References: <008201c6bd7f$04ac6120$2f01a8c0@GOLHARMOBILE1> Message-ID: <36305.81.98.244.247.1155333540.squirrel@webmail.ebi.ac.uk> Each time a new EMBOSS version is released the EMBASSY packages are reconstructed: the EMBASSY packages are specific to a given release. You're trying to compile the EMNU supplied with EMBOSS 3.0.0 on EMBOSS 4.0.0. You need to download EMNU again from the ftp server. The version numbers of the EMBASSY packages reflects their internal functionality and not the version of the main package they are linked against. As this seems to be a common gotcha we'll think of altering this for future releases. We will also consider removing EMNU from future releases. It has been superseded by lots of good GUIs out there. HTH Alan From golharam at umdnj.edu Mon Aug 14 00:33:06 2006 From: golharam at umdnj.edu (Ryan Golhar) Date: Sun, 13 Aug 2006 20:33:06 -0400 Subject: [EMBOSS] Compiling EMNU fails with EMBOSS 4.0.0 In-Reply-To: <36305.81.98.244.247.1155333540.squirrel@webmail.ebi.ac.uk> Message-ID: <002901c6bf39$37e0fa90$2f01a8c0@GOLHARMOBILE1> It might not be a bad idea, or else there is no indication that a new version is available... -----Original Message----- From: ajb at ebi.ac.uk [mailto:ajb at ebi.ac.uk] Sent: Friday, August 11, 2006 5:59 PM To: golharam at umdnj.edu Cc: emboss at lists.open-bio.org Subject: Re: [EMBOSS] Compiling EMNU fails with EMBOSS 4.0.0 Each time a new EMBOSS version is released the EMBASSY packages are reconstructed: the EMBASSY packages are specific to a given release. You're trying to compile the EMNU supplied with EMBOSS 3.0.0 on EMBOSS 4.0.0. You need to download EMNU again from the ftp server. The version numbers of the EMBASSY packages reflects their internal functionality and not the version of the main package they are linked against. As this seems to be a common gotcha we'll think of altering this for future releases. We will also consider removing EMNU from future releases. It has been superseded by lots of good GUIs out there. HTH Alan From rls at ebi.ac.uk Mon Aug 14 07:28:11 2006 From: rls at ebi.ac.uk (Rodrigo Lopez) Date: Mon, 14 Aug 2006 08:28:11 +0100 Subject: [EMBOSS] Compiling EMNU fails with EMBOSS 4.0.0 In-Reply-To: <002901c6bf39$37e0fa90$2f01a8c0@GOLHARMOBILE1> References: <002901c6bf39$37e0fa90$2f01a8c0@GOLHARMOBILE1> Message-ID: <44E0260B.7020100@ebi.ac.uk> FYI: Des Higgins is planning to release a new version of clustalw ca. end 2006. R:) Ryan Golhar wrote: > It might not be a bad idea, or else there is no indication that a new > version is available... > > -----Original Message----- > From: ajb at ebi.ac.uk [mailto:ajb at ebi.ac.uk] > Sent: Friday, August 11, 2006 5:59 PM > To: golharam at umdnj.edu > Cc: emboss at lists.open-bio.org > Subject: Re: [EMBOSS] Compiling EMNU fails with EMBOSS 4.0.0 > > > Each time a new EMBOSS version is released the EMBASSY packages are > reconstructed: the EMBASSY packages are specific to a given release. > > You're trying to compile the EMNU supplied with EMBOSS 3.0.0 on EMBOSS > 4.0.0. You need to download EMNU again from the ftp server. > > The version numbers of the EMBASSY packages reflects their internal > functionality and not the version of the main package they are linked > against. As this seems to be a common gotcha we'll think of altering > this for future releases. > > We will also consider removing EMNU from future releases. It has been > superseded by lots of good GUIs out there. > > HTH > > Alan > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From maoj at helix.nih.gov Mon Aug 14 19:23:04 2006 From: maoj at helix.nih.gov (Jean Mao) Date: Mon, 14 Aug 2006 15:23:04 -0400 Subject: [EMBOSS] Problem installing EMBOSS-4.0.0 on SGI system Message-ID: <000001c6bfd7$11112d10$be4de780@CIT.NIH.GOV> Hi, I received the error message below while trying to install the package on our SGI running irix 6.5.28. We successfully installed version 3.0.0 previously without problem. Could anyone help me ? Thank you very much in advance! % make ??? ??. /bin/sh ../libtool --tag=CC --mode=link cc -Wl,-LD_MSG:off=85:off=84:off=16:off=134 -O3 -o aaindexextract aaindexextract.o ../nucleus/libnucleus.la ../ajax/libajaxg.la ../ajax/libajax.la ../plplot/libplplot.la -L/usr/lib -lX11 -lm mkdir .libs cc -Wl,-LD_MSG:off=85:off=84:off=16:off=134 -O3 -o .libs/aaindexextract aaindexextract.o ../nucleus/.libs/libnucleus.so ../ajax/.libs/libajaxg.so ../ajax/.libs/libajax.so ../plplot/.libs/libplplot.so -L/usr/lib -lX11 -lm -Wl,-rpath -Wl,/usr/localapps/EMBOSS-4.0.0/lib ld32: FATAL 12 : Expecting n32 objects: /usr/lib/crt1.o is o32. *** Error code 2 (bu21) *** Error code 1 (bu21) *** Error code 1 (bu21) % Jean From ajb at ebi.ac.uk Mon Aug 14 21:01:59 2006 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Mon, 14 Aug 2006 22:01:59 +0100 (BST) Subject: [EMBOSS] Problem installing EMBOSS-4.0.0 on SGI system In-Reply-To: <000001c6bfd7$11112d10$be4de780@CIT.NIH.GOV> References: <000001c6bfd7$11112d10$be4de780@CIT.NIH.GOV> Message-ID: <55530.81.98.244.247.1155589319.squirrel@webmail.ebi.ac.uk> Hi Jean, That error usually suggests that the linker would have much preferred to be looking in /usr/lib32. Did you use the --with-sgiabi configuration switch? That would usually make sure that the library path is set up correctly. The syntax is --with-sgiabi=xxxxx where xxxxx is: n32m3 n32m4 64m3 or 64m4 Do a "make clean" before configuring again. Alan From golharam at umdnj.edu Thu Aug 17 19:14:37 2006 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 17 Aug 2006 15:14:37 -0400 Subject: [EMBOSS] EMBOSS 4.0.0 RPMs Message-ID: <023001c6c231$626351a0$2f01a8c0@GOLHARMOBILE1> I've built RPMs for EMBOSS 4.0.0 and related applications. Is there a place I can put them formally? They are available from http://serine.umdnj.edu/~golharam/biorpms Ryan From jison at ebi.ac.uk Fri Aug 18 09:39:27 2006 From: jison at ebi.ac.uk (Jon Ison) Date: Fri, 18 Aug 2006 10:39:27 +0100 (BST) Subject: [EMBOSS] EMBOSS 4.0.0 RPMs In-Reply-To: <023001c6c231$626351a0$2f01a8c0@GOLHARMOBILE1> References: <023001c6c231$626351a0$2f01a8c0@GOLHARMOBILE1> Message-ID: <1310.84.92.187.247.1155893967.squirrel@webmail.ebi.ac.uk> Thanks Ryan I can put them on the EMBOSS ftp site and point to them from the website, on Monday, if that would suit. I'll let you know where the links are. Cheers Jon > I've built RPMs for EMBOSS 4.0.0 and related applications. Is there a > place I can put them formally? > > They are available from http://serine.umdnj.edu/~golharam/biorpms > > Ryan > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From haruosuz at yahoo.co.jp Sun Aug 20 07:38:40 2006 From: haruosuz at yahoo.co.jp (haruosuz at yahoo.co.jp) Date: Sun, 20 Aug 2006 00:38:40 -0700 Subject: [EMBOSS] emboss_4.0.0-2 Message-ID: <4813B756-1E2C-4E77-A491-A5CB4E81EDD2@yahoo.co.jp> Dear Sir: I installed emboss_4.0.0-2, but any commands (e.g., wossname) did not work, as follows: -------------------------------------------- $fink install emboss Information about 5218 packages read in 1 seconds. The following package will be installed or updated: emboss /sw/bin/dpkg-lockwait -i /sw/fink/dists/unstable/main/binary-darwin- i386/sci/emboss_4.0.0-2_darwin-i386.deb $wossname dyld: Library not loaded: /usr/local/lib/libnucleus.3.dylib Referenced from: /usr/local/bin/wossname Reason: image not found Trace/BPT trap -------------------------------------------- [About my Mac] Mac OS X 10.4.6; Darwin 8.6.1; MacBookPro1,1; Intel Core Duo I am looking forward to hearing from you. Sincerely yours, Haruo Suzuki -------------------------------------- Let's start Yahoo! Auction - Free Campaign Now! http://pr.mail.yahoo.co.jp/auction/ From kvddrift at earthlink.net Sun Aug 20 09:29:00 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sun, 20 Aug 2006 05:29:00 -0400 Subject: [EMBOSS] emboss_4.0.0-2 In-Reply-To: <4813B756-1E2C-4E77-A491-A5CB4E81EDD2@yahoo.co.jp> References: <4813B756-1E2C-4E77-A491-A5CB4E81EDD2@yahoo.co.jp> Message-ID: <63DDA3CE-E18A-4373-A518-BA1C168311FA@earthlink.net> On Aug 20, 2006, at 3:38 AM, haruosuz at yahoo.co.jp wrote: > dyld: Library not loaded: /usr/local/lib/libnucleus.3.dylib You seem to have another emboss installation outside fink. Remove that first, and then try again. You may have to rebuild emboss to get it to work. - Koen. From sea99.wang at gmail.com Wed Aug 23 13:01:20 2006 From: sea99.wang at gmail.com (Sea) Date: Wed, 23 Aug 2006 21:01:20 +0800 Subject: [EMBOSS] Installation problems of EMBOSS explorer In-Reply-To: <4f3a50530608230324r886b255lebbe7ab5fe3ae873@mail.gmail.com> References: <4f3a50530608230324r886b255lebbe7ab5fe3ae873@mail.gmail.com> Message-ID: <4f3a50530608230601x4bf1a55cwa44d3dc9605a850e@mail.gmail.com> Hi, This is my first time to install EMBOSS explorer, but I couldn't install successfully. It showed some error messages and seem problems about the perl module. Because I used a non-root-privilege account to do the thing and installed a non-default directory, I'm not sure whether it caused that results. Would any experienced friends tell me some hints? Thanks a lot! :-) From maoj at helix.nih.gov Wed Aug 23 14:19:42 2006 From: maoj at helix.nih.gov (Jean Mao) Date: Wed, 23 Aug 2006 10:19:42 -0400 Subject: [EMBOSS] Question regarding 'showdb' in EMBOSS Message-ID: <000001c6c6bf$2d577f80$be4de780@CIT.NIH.GOV> Hi, I have a question hopefully someone could help me. We have a very hetergenous system which are composed of different platforms. They can all access a shared area where I installed EMBOSS 4.0. The databases are sync'd from area A (both read and writable) to area B (Readable but not writable). When I run 'showdb' on platform A which access databases in area A, I can see the output just fine without any strange message. However, when I run 'showdb' on platform B can access databases in area B, I saw % showdb Displays information on the currently available databases # Name Type ID Qry All Comment # ============ ==== == === === ======= monthaa P OK OK OK - monthnt N OK OK OK - EMBOSS An error in ajfile.c at line 1272: File close problem in fileClose I tried: % showdb -debug But saw the same thing as above without extra information: Displays information on the currently available databases # Name Type ID Qry All Comment # ============ ==== == === === ======= monthaa P OK OK OK - monthnt N OK OK OK - EMBOSS An error in ajfile.c at line 1272: File close problem in fileClose I am not sure why I see this error although the databases were listed just fine. The only thing I can think of is that the databases are located differently. Both .embossrc file and emboss.default file are located in shared area. Could someone give me some hint where this error might come from? Thank you very much! Jean From pmr at ebi.ac.uk Wed Aug 23 15:14:40 2006 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Wed, 23 Aug 2006 16:14:40 +0100 (BST) Subject: [EMBOSS] Question regarding 'showdb' in EMBOSS In-Reply-To: <000001c6c6bf$2d577f80$be4de780@CIT.NIH.GOV> References: <000001c6c6bf$2d577f80$be4de780@CIT.NIH.GOV> Message-ID: <4850.86.141.183.154.1156346080.squirrel@webmail.ebi.ac.uk> Hi Jean, > We have a very hetergenous system which are composed of different > platforms. They can all access a shared area where I installed EMBOSS 4.0. > The databases are sync'd from area A (both read and writable) to area B > (Readable but not writable). When I run 'showdb' on platform A which > access databases in area A, I can see the output just fine without any > strange message. However, when I run 'showdb' on platform B can access > databases in area B, I saw > > % showdb > Displays information on the currently available databases > # Name Type ID Qry All Comment > # ============ ==== == === === ======= > monthaa P OK OK OK - > monthnt N OK OK OK - > > EMBOSS An error in ajfile.c at line 1272: > File close problem in fileClose Curious. The error suggests that the fclose call returned an error. We do not trap the exact error. I will look into ways to get a better error report so we can see what the problem is. > I tried: > > % showdb -debug > > But saw the same thing as above without extra information: -debug creates a file (showdb.dbg) with the debug report. It would be helpful if you can send it to me. regards, Peter Rice From golharam at umdnj.edu Wed Aug 23 15:33:08 2006 From: golharam at umdnj.edu (Ryan Golhar) Date: Wed, 23 Aug 2006 11:33:08 -0400 Subject: [EMBOSS] Installation problems of EMBOSS explorer In-Reply-To: <4f3a50530608230601x4bf1a55cwa44d3dc9605a850e@mail.gmail.com> Message-ID: <004501c6c6c9$6f22b6f0$e6028a0a@GOLHARMOBILE1> What are the errors you are getting? -----Original Message----- From: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Sea Sent: Wednesday, August 23, 2006 9:01 AM To: emboss at lists.open-bio.org Subject: [EMBOSS] Installation problems of EMBOSS explorer Hi, This is my first time to install EMBOSS explorer, but I couldn't install successfully. It showed some error messages and seem problems about the perl module. Because I used a non-root-privilege account to do the thing and installed a non-default directory, I'm not sure whether it caused that results. Would any experienced friends tell me some hints? Thanks a lot! :-) _______________________________________________ EMBOSS mailing list EMBOSS at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss From maoj at helix.nih.gov Wed Aug 23 20:40:42 2006 From: maoj at helix.nih.gov (Jean Mao) Date: Wed, 23 Aug 2006 16:40:42 -0400 Subject: [EMBOSS] Question about make use of multiple fields indexing by dbxfasta or dbxflat Message-ID: <000501c6c6f4$66aad770$be4de780@CIT.NIH.GOV> Hello, I need to index swissprot data file from uniprot.org. They have two formats : fasta and flat available. I understand I can specify fields to be indexed. And there are more fields can be specified if using flat file with dbxflat. However, I am not sure how many programs in EMBOSS package will be benefit from specifying extra fields other than acc and id except 'seqret'? Could someone let me know how to find the answer? Thanks you very much in advance. Jean From sea99.wang at gmail.com Fri Aug 25 03:48:37 2006 From: sea99.wang at gmail.com (Sea) Date: Fri, 25 Aug 2006 11:48:37 +0800 Subject: [EMBOSS] Installation problems of EMBOSS explorer In-Reply-To: <004501c6c6c9$6f22b6f0$e6028a0a@GOLHARMOBILE1> References: <4f3a50530608230601x4bf1a55cwa44d3dc9605a850e@mail.gmail.com> <004501c6c6c9$6f22b6f0$e6028a0a@GOLHARMOBILE1> Message-ID: <4f3a50530608242048u7f978211se5df35673cd5a20e@mail.gmail.com> Hi Ryan, Here is the error shown: server: emboss [source/emboss-explorer]> ./install installing EMBOSS Explorer perl modules... Warning: prerequisite Mail::Send failed to load: Can't locate Mail/Send.pm in @INC (@INC contains: /usr/perl5/5.6.1/lib/sun4-solaris-64int /usr/perl5/5.6.1/lib /usr/perl5/site_perl/5.6.1/sun4-solaris-64int /usr/perl5/site_perl/5.6.1 /usr/perl5/site_perl /usr/perl5/vendor_perl/5.6.1/sun4-solaris-64int /usr/perl5/vendor_perl/5.6.1 /usr/perl5/vendor_perl .) at (eval 4) line 3. Warning: prerequisite Parse::RecDescent failed to load: Can't locate Parse/RecDescent.pm in @INC (@INC contains: /usr/perl5/5.6.1/lib/sun4-solaris-64int /usr/perl5/5.6.1/lib /usr/perl5/site_perl/5.6.1/sun4-solaris-64int /usr/perl5/site_perl/5.6.1 /usr/perl5/site_perl /usr/perl5/vendor_perl/5.6.1/sun4-solaris-64int /usr/perl5/vendor_perl/5.6.1 /usr/perl5/vendor_perl .) at (eval 5) line 3. 'PREREQ_FATAL' is not a known MakeMaker parameter name. Writing Makefile for EMBOSS::GUI Manifying blib/man3/EMBOSS::GUI.3 Manifying blib/man3/EMBOSS::GUI::XHTML.3 Manifying blib/man3/EMBOSS::GUI::Conf.3 Manifying blib/man3/EMBOSS::ACD.3 Manifying blib/man3/EMBOSS::GUI.3 Warning: You do not have permissions to install into /usr/perl5/site_perl/5.6.1/sun4-solaris-64int at /usr/perl5/5.6.1/lib/ExtUtils/Install.pm line 85. mkdir /usr/perl5/site_perl/5.6.1/EMBOSS: Permission denied at /usr/perl5/5.6.1/lib/ExtUtils/Install.pm line 138 *** Error code 255 make: Fatal error: Command failed for target `pure_site_install' I guess that I don't have a root privilege so can't access the /usr/perl5 directory. Thus I installed perl 5.8.5 in my folder and then modified the emboss-explorer "Makefile", but still failed. Hope any experienced friends give me some suggestions. :-) Thank you! On 8/23/06, Ryan Golhar wrote: > What are the errors you are getting? > > -----Original Message----- > From: emboss-bounces at lists.open-bio.org > [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Sea > Sent: Wednesday, August 23, 2006 9:01 AM > To: emboss at lists.open-bio.org > Subject: [EMBOSS] Installation problems of EMBOSS explorer > > > Hi, > > This is my first time to install EMBOSS explorer, > but I couldn't install successfully. > > It showed some error messages and seem problems about the perl module. > > Because I used a non-root-privilege account to do the thing and > installed a non-default directory, I'm not sure whether it caused that > results. > > Would any experienced friends tell me some hints? > > Thanks a lot! :-) > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From aengus.stewart at cancer.org.uk Fri Aug 25 08:34:43 2006 From: aengus.stewart at cancer.org.uk (Aengus Stewart) Date: Fri, 25 Aug 2006 09:34:43 +0100 Subject: [EMBOSS] Jemboss - fuzzpro main panel Message-ID: <44EEB623.8050805@cancer.org.uk> Hi, Sorry I have a problem with Jemboss - the panel for fuzzpro only has a box for "input sequence" there is no way to enter a pattern! fuzzpro runs correctly at the command line. Is there a set of files that define the panel interfaces? Have I managed to mangle these or are they wrong? How do I get/build a new set? Aengus -- ----------------------------------------------------------------------- Aengus Stewart Group Leader Bioinformatics and BioStatistics Tel: +44 (0)20 7269 3679 Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK ----------------------------------------------------------------------- This electronic message contains information which may be privileged and confidential. The information is intended to be for the use of the individual(s) or entity named above. Be aware that any third party disclosure, distribution, copying or use of this communication, without prior permission, is strictly prohibited. From tjc at sanger.ac.uk Fri Aug 25 11:36:28 2006 From: tjc at sanger.ac.uk (Tim Carver) Date: Fri, 25 Aug 2006 12:36:28 +0100 Subject: [EMBOSS] Jemboss - fuzzpro main panel In-Reply-To: <44EEB623.8050805@cancer.org.uk> Message-ID: Hi Aengus This is a problem in the current EMBOSS release. I have committed a temporary fix in CVS. Regards Tim On 25/8/06 09:34, "Aengus Stewart" wrote: > Hi, > > Sorry I have a problem with Jemboss - the panel for fuzzpro only has a box for > "input sequence" there is no way to enter a pattern! fuzzpro runs correctly > at the command line. > > Is there a set of files that define the panel interfaces? Have I managed to > mangle these or are they wrong? How do I get/build a new set? > > > Aengus From pmr at ebi.ac.uk Fri Aug 25 13:59:50 2006 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 25 Aug 2006 14:59:50 +0100 Subject: [EMBOSS] EMBOSS 4.0.0 Latest Fixes Message-ID: <44EF0256.1040802@ebi.ac.uk> I have posted some further fixes on the EMBOSS FTP site. None are critical. Users have been reporting interesting bugs. Some were also in release 3.0.0. The fuzznuc, fuzzpro and fuzztran reports were changed in 4.0.0 to always report something. Unfortunately users running searches over the whole database found their output files were very large. We have changed the way reports work as follows: 1. fuzznuc, fuzzpro and fuzztran again report only sequences with hits 2. when a report is closed, a default header and footer are written (solving the problem of empty output files) 3. for sites that had concerns about searches for trivial patterns taking too long and generating too much output, reports have 2 new associated qualifiers. -rmaxall limits the total number of matches reported (fuzznuc, fuzzpro and fuzztran terminate when the limit is reached), -rmaxseq limits the maximum number of hits for one sequence. We also have various fixes for reporting matches on the reverse strand, and for improved parsing of FASTA file IDs. To update your EMBOSS 4.0.0 release, go to: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/ File README.fixes (see below) lists the files and describes the fixes. Copy the files to the indicated directories and reinstall. regards, Peter Rice file README.fixes 25-aug-2006 The files in this directory are bugfix replacements for files in the EMBOSS-4.0.0 distribution. Just drop the replacement files in the location shown and redo the 'make install.' Fix 1. EMBOSS-4.0.0/nucleus/embpatlist.c 31 Jul 2006: Fixes a problem with searching for patterns and regular expression in the reverse strand of nucleotide sequences. The change is to use ajSeqReverseForce (always reverses the sequence provided) instead of ajSeqReverseDo (which only reverses if the reverse flag is set) 9 Aug 2006: Revised to also fix a problem with reverse strand sequence positions. Fix 2. EMBOSS-4.0.0/ajax/ajfile.c 31 Jul 2006: This fixes a bug where deleting the last line of buffered input fails to reset the pointer to the last buffered line. This only affected debug traces. Unfortunately, the ajFileBuffClear function does call the debug trace. In practice we have only seen this bug when processing sequence data in EMBL format from an MRS server. Fix 3. EMBOSS-4.0.0/ajax/ajnam.c 31 Jul 3006: New database access methods MRS and DBFETCH need to be explicitly turned on so that showdb can report them. Fix 4. EMBOSS-4.0.0/ajax/ajseqdb.c 31 Jul 2006: The new MRS access method used a general search. This gave strange results when the ID or accession appeared in any other entry. It appears that MRS can search for id or accession only. This worked on the main MRS server at least. MRS access will be further extended in the next release. Please contact the developers emboss-bug at emboss.open-bio.org if you would like to help test new features in MRS access. 25 Aug 2006: Further change to allow multiple %s replacements in complex URLs for access method URL. Needed for complex SRS queries to resolve EMBL IDs so the following definition can be used for EMBL (warning, the URL may wrap badly in this email!) DB embl [ method: "url" format: "embl" type: "N" url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-noSession+-ascii+-vn+2+-e+[embl-id:%s]|[embl-acc:%s]|([emblidacc-id:%s]>embl)" comment: "EMBL from SRS including old IDs" ] Fix 5. EMBOSS-4.0.0/configure 07 Aug 2006: Fix configuration problem on Intel Mac machines. Make sure this file is executable (chmod 755 configure) after downloading it. Fix 6. EMBOSS-4.0.0/ajax/ajseq.c 09 Aug 2006: Return correct USA for "asis::" sequence input. Fix 7. EMBOSS-4.0.0/emboss/dreg.c 09 Aug 2006: Correct sequence positions on the reverse strand. Fix 8. See Fix 13 Fix 9. See Fix 13 Fix10. EMBOSS-4.0.0/doc/programs/html/banana.1.banana.gif EMBOSS-4.0.0/doc/programs/html/tcode.2.tcode.gif 14 Aug 2006: These graphics example outputs were missing from the distribution. When you run make install they will be copied to the installed documentation. Fix 11. EMBOSS-4.0.0/emboss/merger.c EMBOSS-4.0.0/emboss/needle.c EMBOSS-4.0.0/emboss/prophet.c EMBOSS-4.0.0/emboss/water.c 14 Aug 2006: These programs calculate an internal path size from the lengths of the input sequences. For sequences that are too long, a fatal error is produced. But if the sequences are extremely long, the test failed and the program gave a segmentation fault. This fix tests in a different way that will catch all cases. Fix 12. See Fix13 Fix 13. EMBOSS-4.0.0/ajax/ajacd.c EMBOSS-4.0.0/ajax/ajfeat.c EMBOSS-4.0.0/ajax/ajfeat.h EMBOSS-4.0.0/ajax/ajreport.c EMBOSS-4.0.0/ajax/ajreport.h EMBOSS-4.0.0/emboss/fuzznuc.c EMBOSS-4.0.0/emboss/fuzzpro.c EMBOSS-4.0.0/emboss/fuzztran.c 21 Aug 2006: This provides new qualifiers to limit report output to a number of hits in total (-rmaxall) or for any one sequence (-rmaxseq). It also fixes reversed feature locations for reports in EMBL format. The files fixed overlap with earlier fixes which are included here. 09 Aug 2006: Fix 8: In release 4.0.0 these 3 programs were changed to report even when no hits were found. The aim was to avoid empty output for a single sequence. Many users were running these programs over large input sets, and now get excessively large output files. The change has been reversed. Fix 9 makes sure a small output file is produced when no hits are found. 09 Aug 2006: Fix 9: When closing a report (with ajReportClose) make sure a standard report header and footer are printed if nothing has been reported so far. The header reports the command line. The new footer reports the total number of sequences and features reported. Reversed sequence positions are corrected for listfile report format. No header can be reported for some formats (EMBL, Genbank, GFF, PIR, Swiss, Excel, Feattable). 14 Aug 2006: Fix12: This fixes a bug where putting -ofopenfile on the command line for features output failed to set the feature output format. Fix 14. EMBOSS-4.0.0/ajax/ajseqread.c EMBOSS-4.0.0/ajax/ajseqread.h EMBOSS-4.0.0/ajax/ajseqwrite.c EMBOSS-4.0.0/emboss/dbiblast.c EMBOSS-4.0.0/emboss/dbifasta.c EMBOSS-4.0.0/emboss/dbxfasta.c EMBOSS-4.0.0/emboss/acd/dbiblast.acd EMBOSS-4.0.0/emboss/acd/dbifasta.acd EMBOSS-4.0.0/emboss/acd/dbxfasta.acd 24 Aug 2006: Pearson format preserves dbname:entryname style IDs NCBI format parsing (includes FASTA format parsing) extracts database name from NCBI piped ids and uses on output unless EMBOSS has defined some other database name. Three indexing programs call the NCBI parsing function which has an extra argument. Fasta parsing was also modified to allow UniProt style (yet another FASTA format) where the accession number is in brackets. The "idacc" default format now removes brackets before checking for an accession number or version next on the line. From golharam at umdnj.edu Fri Aug 25 15:25:30 2006 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 25 Aug 2006 11:25:30 -0400 Subject: [EMBOSS] Installation problems of EMBOSS explorer In-Reply-To: <4f3a50530608242048u7f978211se5df35673cd5a20e@mail.gmail.com> Message-ID: <006101c6c85a$b39f6f20$2f01a8c0@GOLHARMOBILE1> It looks like you need to install other perl modules includes Mail::Send, and Parse::RecDescent. If you don't have root permission to install, then you can install in a local directory. I *think* the command is 'make DESTDIR=/home/sea/perl5.8.5 install' where DESTDIR is the variable to indicate the installation root. Ryan -----Original Message----- From: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Sea Sent: Thursday, August 24, 2006 11:49 PM To: emboss at lists.open-bio.org Subject: Re: [EMBOSS] Installation problems of EMBOSS explorer Hi Ryan, Here is the error shown: server: emboss [source/emboss-explorer]> ./install installing EMBOSS Explorer perl modules... Warning: prerequisite Mail::Send failed to load: Can't locate Mail/Send.pm in @INC (@INC contains: /usr/perl5/5.6.1/lib/sun4-solaris-64int /usr/perl5/5.6.1/lib /usr/perl5/site_perl/5.6.1/sun4-solaris-64int /usr/perl5/site_perl/5.6.1 /usr/perl5/site_perl /usr/perl5/vendor_perl/5.6.1/sun4-solaris-64int /usr/perl5/vendor_perl/5.6.1 /usr/perl5/vendor_perl .) at (eval 4) line 3. Warning: prerequisite Parse::RecDescent failed to load: Can't locate Parse/RecDescent.pm in @INC (@INC contains: /usr/perl5/5.6.1/lib/sun4-solaris-64int /usr/perl5/5.6.1/lib /usr/perl5/site_perl/5.6.1/sun4-solaris-64int /usr/perl5/site_perl/5.6.1 /usr/perl5/site_perl /usr/perl5/vendor_perl/5.6.1/sun4-solaris-64int /usr/perl5/vendor_perl/5.6.1 /usr/perl5/vendor_perl .) at (eval 5) line 3. 'PREREQ_FATAL' is not a known MakeMaker parameter name. Writing Makefile for EMBOSS::GUI Manifying blib/man3/EMBOSS::GUI.3 Manifying blib/man3/EMBOSS::GUI::XHTML.3 Manifying blib/man3/EMBOSS::GUI::Conf.3 Manifying blib/man3/EMBOSS::ACD.3 Manifying blib/man3/EMBOSS::GUI.3 Warning: You do not have permissions to install into /usr/perl5/site_perl/5.6.1/sun4-solaris-64int at /usr/perl5/5.6.1/lib/ExtUtils/Install.pm line 85. mkdir /usr/perl5/site_perl/5.6.1/EMBOSS: Permission denied at /usr/perl5/5.6.1/lib/ExtUtils/Install.pm line 138 *** Error code 255 make: Fatal error: Command failed for target `pure_site_install' I guess that I don't have a root privilege so can't access the /usr/perl5 directory. Thus I installed perl 5.8.5 in my folder and then modified the emboss-explorer "Makefile", but still failed. Hope any experienced friends give me some suggestions. :-) Thank you! On 8/23/06, Ryan Golhar wrote: > What are the errors you are getting? > > -----Original Message----- > From: emboss-bounces at lists.open-bio.org > [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Sea > Sent: Wednesday, August 23, 2006 9:01 AM > To: emboss at lists.open-bio.org > Subject: [EMBOSS] Installation problems of EMBOSS explorer > > > Hi, > > This is my first time to install EMBOSS explorer, > but I couldn't install successfully. > > It showed some error messages and seem problems about the perl module. > > Because I used a non-root-privilege account to do the thing and > installed a non-default directory, I'm not sure whether it caused that > results. > > Would any experienced friends tell me some hints? > > Thanks a lot! :-) > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss _______________________________________________ EMBOSS mailing list EMBOSS at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss From mthon at tamu.edu Fri Aug 25 21:31:41 2006 From: mthon at tamu.edu (Michael Thon) Date: Fri, 25 Aug 2006 16:31:41 -0500 Subject: [EMBOSS] EMBOSS 4.0.0 Latest Fixes In-Reply-To: <44EF0256.1040802@ebi.ac.uk> References: <44EF0256.1040802@ebi.ac.uk> Message-ID: <005A5F53-7C8E-49CB-9AEA-B34C13053B0A@tamu.edu> Hi Peter - Will you be releasing an update to the emboss distribution that includes these changes? cheers Mike On Aug 25, 2006, at 8:59 AM, Peter Rice wrote: > I have posted some further fixes on the EMBOSS FTP site. None are > critical. Users have been reporting interesting bugs. Some were > also in > release 3.0.0. > > The fuzznuc, fuzzpro and fuzztran reports were changed in 4.0.0 to > always report something. Unfortunately users running searches over the > whole database found their output files were very large. We have > changed > the way reports work as follows: > > 1. fuzznuc, fuzzpro and fuzztran again report only sequences with hits > > 2. when a report is closed, a default header and footer are written > (solving the problem of empty output files) > > 3. for sites that had concerns about searches for trivial patterns > taking too long and generating too much output, reports have 2 new > associated qualifiers. -rmaxall limits the total number of matches > reported (fuzznuc, fuzzpro and fuzztran terminate when the limit is > reached), -rmaxseq limits the maximum number of hits for one sequence. > > We also have various fixes for reporting matches on the reverse > strand, > and for improved parsing of FASTA file IDs. > > To update your EMBOSS 4.0.0 release, go to: > > ftp://emboss.open-bio.org/pub/EMBOSS/fixes/ > > File README.fixes (see below) lists the files and describes the fixes. > > Copy the files to the indicated directories and reinstall. > > regards, > > Peter Rice > > file README.fixes 25-aug-2006 > > The files in this directory are bugfix replacements for files in > the EMBOSS-4.0.0 distribution. Just drop the replacement files in > the location shown and redo the 'make install.' > > > Fix 1. EMBOSS-4.0.0/nucleus/embpatlist.c > > 31 Jul 2006: Fixes a problem with searching for patterns and regular > expression in the reverse strand of nucleotide sequences. The change > is to use ajSeqReverseForce (always reverses the sequence provided) > instead of ajSeqReverseDo (which only reverses if the reverse flag is > set) > > 9 Aug 2006: Revised to also fix a problem with reverse strand sequence > positions. > > > Fix 2. EMBOSS-4.0.0/ajax/ajfile.c > > 31 Jul 2006: This fixes a bug where deleting the last line of buffered > input fails to reset the pointer to the last buffered line. This only > affected debug traces. Unfortunately, the ajFileBuffClear function > does call the debug trace. In practice we have only seen this bug when > processing sequence data in EMBL format from an MRS server. > > Fix 3. EMBOSS-4.0.0/ajax/ajnam.c > > 31 Jul 3006: New database access methods MRS and DBFETCH need to be > explicitly turned on so that showdb can report them. > > > Fix 4. EMBOSS-4.0.0/ajax/ajseqdb.c > > 31 Jul 2006: The new MRS access method used a general search. This > gave strange results when the ID or accession appeared in any other > entry. It appears that MRS can search for id or accession only. This > worked on the main MRS server at least. > > MRS access will be further extended in the next release. Please > contact the developers emboss-bug at emboss.open-bio.org if you would > like to help test new features in MRS access. > > 25 Aug 2006: Further change to allow multiple %s replacements in > complex URLs for access method URL. Needed for complex SRS queries to > resolve EMBL IDs so the following definition can be used for EMBL > (warning, the URL may wrap badly in this email!) > > DB embl [ > method: "url" > format: "embl" > type: "N" > url: > > "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-noSession+-ascii+-vn+2+- > e+[embl-id:%s]|[embl-acc:%s]|([emblidacc-id:%s]>embl)" > comment: "EMBL from SRS including old IDs" > ] > > Fix 5. EMBOSS-4.0.0/configure > > 07 Aug 2006: Fix configuration problem on Intel Mac machines. Make > sure > this file is executable (chmod 755 configure) after downloading it. > > Fix 6. EMBOSS-4.0.0/ajax/ajseq.c > > 09 Aug 2006: Return correct USA for "asis::" sequence input. > > Fix 7. EMBOSS-4.0.0/emboss/dreg.c > > 09 Aug 2006: Correct sequence positions on the reverse strand. > > Fix 8. See Fix 13 > > Fix 9. See Fix 13 > > Fix10. EMBOSS-4.0.0/doc/programs/html/banana.1.banana.gif > EMBOSS-4.0.0/doc/programs/html/tcode.2.tcode.gif > > 14 Aug 2006: These graphics example outputs were missing from the > distribution. When you run make install they will be copied to the > installed documentation. > > Fix 11. EMBOSS-4.0.0/emboss/merger.c > EMBOSS-4.0.0/emboss/needle.c > EMBOSS-4.0.0/emboss/prophet.c > EMBOSS-4.0.0/emboss/water.c > > 14 Aug 2006: These programs calculate an internal path size from the > lengths of the input sequences. For sequences that are too long, a > fatal error is produced. But if the sequences are extremely long, the > test failed and the program gave a segmentation fault. This fix tests > in a different way that will catch all cases. > > Fix 12. See Fix13 > > Fix 13. EMBOSS-4.0.0/ajax/ajacd.c > EMBOSS-4.0.0/ajax/ajfeat.c > EMBOSS-4.0.0/ajax/ajfeat.h > EMBOSS-4.0.0/ajax/ajreport.c > EMBOSS-4.0.0/ajax/ajreport.h > EMBOSS-4.0.0/emboss/fuzznuc.c > EMBOSS-4.0.0/emboss/fuzzpro.c > EMBOSS-4.0.0/emboss/fuzztran.c > > 21 Aug 2006: This provides new qualifiers to limit report output to a > number of hits in total (-rmaxall) or for any one sequence > (-rmaxseq). It also fixes reversed feature locations for reports in > EMBL format. The files fixed overlap with earlier fixes which are > included here. > > 09 Aug 2006: Fix 8: In release 4.0.0 these 3 programs were changed > to report > even when no hits were found. The aim was to avoid empty output for a > single sequence. > > Many users were running these programs over large input sets, and now > get excessively large output files. > > The change has been reversed. Fix 9 makes sure a small output > file is produced when no hits are found. > > 09 Aug 2006: Fix 9: When closing a report (with ajReportClose) make > sure a > standard report header and footer are printed if nothing has been > reported so far. The header reports the command line. The new footer > reports the total number of sequences and features reported. > > Reversed sequence positions are corrected for listfile report format. > > No header can be reported for some formats (EMBL, Genbank, GFF, PIR, > Swiss, Excel, Feattable). > > 14 Aug 2006: Fix12: This fixes a bug where putting -ofopenfile on the > command > line for features output failed to set the feature output format. > > > Fix 14. EMBOSS-4.0.0/ajax/ajseqread.c > EMBOSS-4.0.0/ajax/ajseqread.h > EMBOSS-4.0.0/ajax/ajseqwrite.c > EMBOSS-4.0.0/emboss/dbiblast.c > EMBOSS-4.0.0/emboss/dbifasta.c > EMBOSS-4.0.0/emboss/dbxfasta.c > EMBOSS-4.0.0/emboss/acd/dbiblast.acd > EMBOSS-4.0.0/emboss/acd/dbifasta.acd > EMBOSS-4.0.0/emboss/acd/dbxfasta.acd > > 24 Aug 2006: Pearson format preserves dbname:entryname style IDs > NCBI format parsing (includes FASTA format parsing) extracts database > name from NCBI piped ids and uses on output unless EMBOSS has defined > some other database name. > > Three indexing programs call the NCBI parsing function which has an > extra argument. > > Fasta parsing was also modified to allow UniProt style (yet another > FASTA format) where the accession number is in brackets. The "idacc" > default format now removes brackets before checking for an accession > number or version next on the line. > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From kvddrift at earthlink.net Sat Aug 26 15:05:58 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sat, 26 Aug 2006 11:05:58 -0400 Subject: [EMBOSS] EMBOSS 4.0.0 Latest Fixes In-Reply-To: <44EF0256.1040802@ebi.ac.uk> References: <44EF0256.1040802@ebi.ac.uk> Message-ID: <989F3713-DB05-45C9-9F3D-4CC9D36E4AB4@earthlink.net> On Aug 25, 2006, at 9:59 AM, Peter Rice wrote: > EMBOSS-4.0.0/emboss/acd/dbiblast.acd FYI, this file is not in the fixes directory. Also the file restrict.c is in the fixes directory, but not in the readme. - Koen. From ajb at ebi.ac.uk Sun Aug 27 08:50:11 2006 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Sun, 27 Aug 2006 09:50:11 +0100 (BST) Subject: [EMBOSS] EMBOSS 4.0.0 Latest Fixes In-Reply-To: <989F3713-DB05-45C9-9F3D-4CC9D36E4AB4@earthlink.net> References: <44EF0256.1040802@ebi.ac.uk> <989F3713-DB05-45C9-9F3D-4CC9D36E4AB4@earthlink.net> Message-ID: <55707.81.98.244.247.1156668611.squirrel@webmail.ebi.ac.uk> >> EMBOSS-4.0.0/emboss/acd/dbiblast.acd > > FYI, this file is not in the fixes directory. And, according to CVS, it shouldn't be. I've removed it from the README.fixes file. > Also the file > restrict.c is in the fixes directory, but not in the readme. This concerned the reporting of complementary strand matches in EMBL feature tables. I've appended a note to the README.fixes file. Thanks Alan From ajb at ebi.ac.uk Sun Aug 27 10:32:51 2006 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Sun, 27 Aug 2006 11:32:51 +0100 (BST) Subject: [EMBOSS] EMBOSS 4.0.0 Latest Fixes In-Reply-To: <005A5F53-7C8E-49CB-9AEA-B34C13053B0A@tamu.edu> References: <44EF0256.1040802@ebi.ac.uk> <005A5F53-7C8E-49CB-9AEA-B34C13053B0A@tamu.edu> Message-ID: <50816.81.98.244.247.1156674771.squirrel@webmail.ebi.ac.uk> Dear Michael, > Hi Peter I'll have to do in his absence. :-) > Will you be releasing an update to the emboss distribution > that includes these changes? We're keeping that under review. For now I've put a UNIX 'patch' file on the anonymous ftp server which may make things easier for people. See my next posting. ATB Alan From ajb at ebi.ac.uk Sun Aug 27 10:47:07 2006 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Sun, 27 Aug 2006 11:47:07 +0100 (BST) Subject: [EMBOSS] Updating EMBOSS: patch files Message-ID: <51319.81.98.244.247.1156675627.squirrel@webmail.ebi.ac.uk> As the start of an experimental service, discussed at an EMBOSS developers' meeting, I've created a 'patches' directory on the anonymous ftp server: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/ The purpose of this directory is to provide UNIX 'patch' (context diff) files. These should make EMBOSS easier to update between releases as you only need to apply one patch rather than all the individual fixes from the directory above. This depends on your system having the 'patch' command installed. As it is an experimental service there may be the odd dragon lurking. Let us know if you find one. I append the README.patch file from the above directory which explains how to use the patch files. Alan The file(s) in this directory are standard UNIX 'patch' files and can be used to update the base EMBOSS release with all the fixes given in: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README.fixes The filenames are of the format 'patch-1-X.gz' where 'X' represents the last fix incorporated: so a file called patch-1-10.gz will incorporate fixes from Fix 1 to Fix 10 as given in the README.fixes file. To update the base EMBOSS installation (where x.y.z is the version): 1. Download a fresh EMBOSS-x.y.z.tar.gz and unpack it with gunzip and tar. 2. Download the required patch file. 3. cd EMBOSS-x.y.z 4. gunzip -c /somewhere/patch-1-X.gz | patch -p1 or 1-3 as above 4. gunzip /somewhere/patch-1-X.gz patch -p1 < /somewhere/patch-1-X Then configure EMBOSS as normal. N.B. (27th Aug 2006): This is a new method for providing updates and therefore not tested in anger by the community. Please let us know of any problems. From jgkannan at rediffmail.com Tue Aug 29 07:04:46 2006 From: jgkannan at rediffmail.com (J.G.Kannan) Date: 29 Aug 2006 07:04:46 -0000 Subject: [EMBOSS] Few Queries Message-ID: <20060829070446.14707.qmail@webmail32.rediffmail.com> Hi All, I am newbie to this application. I have few queries mentioned below. It would be great if anyone send me the answers, 1. Dose this application supports parallel computing? 2. EMBOSS supports S10x86 (32 and 64 bit) ? 3. What are programming standards and technology your using? Thanks in advance -J.G.Kannan From shrish at ccmb.res.in Tue Aug 29 11:37:46 2006 From: shrish at ccmb.res.in (Shrish Tiwari) Date: Tue, 29 Aug 2006 18:07:46 +0630 Subject: [EMBOSS] (no subject) Message-ID: Hi! Is there a program in EMBOSS to extract the coordinates of exons? Shrish ______________________________________________________________________ Dr. Shrish Tiwari, Scientist BIC, Centre for Cellular and Molecular Biology Uppal Road, Hyderabad - 500 007 Phone: 91-40-7192776 (work), 91-40-7156603 (home) email: shrish at ccmb.res.in ______________________________________________________________________ From David.Bauer at schering.de Tue Aug 29 13:29:10 2006 From: David.Bauer at schering.de (David.Bauer at schering.de) Date: Tue, 29 Aug 2006 15:29:10 +0200 Subject: [EMBOSS] Antwort: (no subject) In-Reply-To: Message-ID: Hi, you can use 'showfeat' with the option '-pos' to display sequence features with the positions. If your exons are annotated as 'mRNA' in the feature table you could use: showfeat -pos -matchtype mRNA To get only the positions without the ascii graphics use '-width 0' HTH, David. emboss-bounces at lists.open-bio.org schrieb am 29/08/2006 13:37:46: > Hi! > > Is there a program in EMBOSS to extract the coordinates of exons? > > Shrish > > > ______________________________________________________________________ > Dr. Shrish Tiwari, Scientist > BIC, Centre for Cellular and Molecular Biology > Uppal Road, Hyderabad - 500 007 > Phone: 91-40-7192776 (work), 91-40-7156603 (home) > email: shrish at ccmb.res.in > ______________________________________________________________________ > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From simon.andrews at bbsrc.ac.uk Thu Aug 31 10:48:56 2006 From: simon.andrews at bbsrc.ac.uk (Simon Andrews) Date: Thu, 31 Aug 2006 11:48:56 +0100 Subject: [EMBOSS] (no subject) In-Reply-To: References: Message-ID: <8E95A140-DDA1-46C0-9990-5979068E3E57@bbsrc.ac.uk> On 29 Aug 2006, at 12:37, Shrish Tiwari wrote: > Hi! > > Is there a program in EMBOSS to extract the coordinates of exons? It depends what you mean. If you want to extract the transcript sequence from a genomic sequence with an mRNA feature defined in its header then you can use coderet. If you want to figure out where the exon positions are in a sequence and you have an mRNA and a genomic sequence then you can use est2genome. If you just want to view the header annotation then entret will give you that. Simon. From tao.song at calibrant.com Thu Aug 31 15:01:38 2006 From: tao.song at calibrant.com (Tao Song) Date: Thu, 31 Aug 2006 15:01:38 -0000 Subject: [EMBOSS] How to modify a program? References: Message-ID: <001a01c654d4$6bfc13c0$1b02a8c0@tao> Hi, I am new to Unix system, so sorry if it is a too simple question. I need to modify the DIGEST program (\EMBOSS-4.0.0\emboss\digest) to change some rules for trypsin digestion. The part of the program that I need to modify is in another program (EMBOSS-4.0.0\nucleus\embprop.c). After modify the embprop program I compiled with gcc and got a embprop.o file. But when I ran the DIGEST program it still give the same results and didn't change. Are there some steps that I missed? Thanks a lot for your help! Regards, Tao From sbassi at gmail.com Thu Aug 31 15:25:03 2006 From: sbassi at gmail.com (Sebastian Bassi) Date: Thu, 31 Aug 2006 12:25:03 -0300 Subject: [EMBOSS] How to modify a program? In-Reply-To: <001a01c654d4$6bfc13c0$1b02a8c0@tao> References: <001a01c654d4$6bfc13c0$1b02a8c0@tao> Message-ID: On 3/31/06, Tao Song wrote: > change. Are there some steps that I missed? What I did once was to do a new configure and make, that compiled only the changed file (don't ask me how the compiler knew that I changed only one .c file). Also check for path problems (maybe you are executing a version that is in the path before the one you want to run) -- Bioinformatics news: http://www.bioinformatica.info Lriser: http://www.linspire.com/lraiser_success.php?serial=318 From golharam at umdnj.edu Thu Aug 31 18:38:50 2006 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 31 Aug 2006 14:38:50 -0400 Subject: [EMBOSS] Building EMBOSS error Message-ID: <025e01c6cd2c$b564b910$2f01a8c0@GOLHARMOBILE1> Hi, I'm building EMBOSS 4.0.0 (with patch 1-15) on Solaris uname -a: SunOS siriusC 5.8 Generic_117350-38 sun4u sparc SUNW,Sun-Fire When I run the configure script I get: checking for purify... no expr: syntax error ./configure: test: =: unary operator expected checking if any threading type is given... No I'm still able to build fine but wasn't sure if this error might cause some problems... Ryan From ajb at ebi.ac.uk Thu Aug 31 20:18:11 2006 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Thu, 31 Aug 2006 21:18:11 +0100 (BST) Subject: [EMBOSS] Building EMBOSS error In-Reply-To: <025e01c6cd2c$b564b910$2f01a8c0@GOLHARMOBILE1> References: <025e01c6cd2c$b564b910$2f01a8c0@GOLHARMOBILE1> Message-ID: <1089.81.131.22.33.1157055491.squirrel@webmail.ebi.ac.uk> > When I run the configure script I get: > > checking for purify... no > expr: syntax error > ./configure: test: =: unary operator expected > checking if any threading type is given... No > > I'm still able to build fine but wasn't sure if this error might cause > some problems... That is a message which can be safely ignored. I do need to tidy that up though - thanks for the reminder. Alan