From lefranc at ligm.igh.cnrs.fr Wed Jan 2 10:28:19 2002 From: lefranc at ligm.igh.cnrs.fr (Marie-Paule Lefranc) Date: Wed, 02 Jan 2002 16:28:19 +0100 Subject: New IMGT tools freely available at http://imgt.cines.fr Message-ID: <5.1.0.14.1.20020102161051.009f6830@ligm.igh.cnrs.fr> Dear Colleague, I will be grateful if you accepted to diffuse this accompanying announcement so that your members be aware of this new development of IMGT. With many thanks for your help. Best Regards Yours sincerely Marie-Paule Lefranc -------------- next part -------------- A non-text attachment was scrubbed... Name: IMGT news Dec 2001.doc Type: application/msword Size: 28672 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss/attachments/20020102/5fdb6beb/attachment.doc -------------- next part -------------- IMGT, the international ImMunoGeneTics database http://imgt.cines.fr LIGM, IGH, UPR CNRS 1142 141 rue de la Cardonille 34396 Montpellier Cedex 5 FRANCE Tel: +33 (0)4 99 61 99 65 Fax: +33 (0)4 99 61 99 01 From lefranc at ligm.igh.cnrs.fr Wed Jan 2 10:28:19 2002 From: lefranc at ligm.igh.cnrs.fr (Marie-Paule Lefranc) Date: Wed, 02 Jan 2002 16:28:19 +0100 Subject: New IMGT tools freely available at http://imgt.cines.fr Message-ID: <5.1.0.14.1.20020102161051.009f6830@ligm.igh.cnrs.fr> Dear Colleague, I will be grateful if you accepted to diffuse this accompanying announcement so that your members be aware of this new development of IMGT. With many thanks for your help. Best Regards Yours sincerely Marie-Paule Lefranc -------------- next part -------------- A non-text attachment was scrubbed... Name: IMGT news Dec 2001.doc Type: application/msword Size: 28672 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss/attachments/20020102/5fdb6beb/attachment-0001.doc -------------- next part -------------- IMGT, the international ImMunoGeneTics database http://imgt.cines.fr LIGM, IGH, UPR CNRS 1142 141 rue de la Cardonille 34396 Montpellier Cedex 5 FRANCE Tel: +33 (0)4 99 61 99 65 Fax: +33 (0)4 99 61 99 01 From mathog at mendel.bio.caltech.edu Thu Jan 3 14:07:25 2002 From: mathog at mendel.bio.caltech.edu (David Mathog) Date: Thu, 03 Jan 2002 11:07:25 -0800 Subject: 2.1.0 build glitches on Solaris 8 Message-ID: I just tried installing 2.1.0 on Solaris 8. After unpacking it in the top level did: # ./configure --with-png # make and it blew up in the libtool link of plplot complaining about not finding "yes/lib". Turns out plplot/Makefile had CPPFLAGS = -Iyes/include -Iyes LDFLAGS = -Lyes/lib which is seriously wrong. Tried again with gmake and had the same problem. Oops, just realized that make clean doesn't remove Makefile. Take them all out with: # find . -name Makefile -exec rm {} \; # ./configure --with-png and this time plplot/Makefile shows: CPPFLAGS = -I/usr/include -I/usr LDFLAGS = -L/usr/lib and now make for plplot works. Bizarre - some sort of first run initialization problem exists. Unfortunately all is still not working right.. When it hits ajacd.o it blows up with: ajacd.c: In function `acdBadVal': ajacd.c:2827: `__builtin_va_alist' undeclared (first use in this function) ajacd.c:2827: (Each undeclared identifier is reported only once ajacd.c:2827: for each function it appears in.) ajacd.c: In function `acdLog': ajacd.c:13323: `__builtin_va_alist' undeclared (first use in this function) ajacd.c: In function `acdPretty': ajacd.c:13359: `__builtin_va_alist' undeclared (first use in this function) *** Error code 1 make: Fatal error: Command failed for target `ajacd.lo' Current working directory /usr/local/src/EMBOSS-2.1.0/ajax *** Error code 1 make: Fatal error: Command failed for target `all-recursive' This was using gcc version 2.95.3 20010315 (release). I've seen problems with that builtin before, but usually it's the other way around - conflicting definitions when gcc uses certain includes. Here it looks like those includes were left out. Try once more using the native (Forte) compiler (which is how I built the 1.12.0 version) # make clean # find . -name Makefile -exec rm {} \; # export CC=cc # echo $CC cc # ./configure --with-png RATS - it rejects the png stuff this time with: checking if png driver is wanted... yes checking for inflateEnd in -lz... yes checking for png_destroy_read_struct in -lpng... no No png driver will be made due to librarys missing/old. continue on anyway to see if this resolves the builtin problem... Yes, apparently using the Forte compiler takes care of the va_builtin problem - at the cost of losing the PNG device. The Forte compiler is: Sun WorkShop 6 update 1 C 5.2 2000/09/11 Somebody must have this working on Solaris. What is the magic incantation to get a full build with PNG enabled??? Thanks, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From ableasby at hgmp.mrc.ac.uk Thu Jan 3 15:05:01 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Thu, 3 Jan 2002 20:05:01 GMT Subject: 2.1.0 build glitches on Solaris 8 Message-ID: <200201032005.UAA20974@bromine.hgmp.mrc.ac.uk> The --with-png really should be --with-pngdriver=directory Assuming you have libpng* in /foo/bar/lib then 'directory' should be /foo/bar (the /lib is assumed to be essential). If the configure can find the libpng, libz and libgd libraries in a standard place it will automatically include png support. Standard places are generally /usr/lib and /usr/local/lib If you don't specify a directory then the default value of --with-png is "yes" hence the problem (at least that is what I suspect). If your gd,z & png are not all in a standard place then it may help to put them all in the same lib directory somewhere. The command ./configure --help is useful for the syntax. As for the varargs messages. That is a fairly well known problem with some installations of gcc on Solaris. It is a difficult one for the configure scripts to resolve satisfactorily. The easiest dirty hack would be to edit ajax/Makefile and delete all occurrences of '-I/usr/include' since then there will be no conflicts between the standard and GNU varargs headers. Alan From mathog at mendel.bio.caltech.edu Thu Jan 3 15:18:19 2002 From: mathog at mendel.bio.caltech.edu (David Mathog) Date: Thu, 03 Jan 2002 12:18:19 -0800 Subject: EMNU build under EMBOSS 2.1.0 Message-ID: Trying to get EMBASSY bits working under EMBOSS 2.1.0 on Solaris 8 (following mostly successful build of EMBOSS 2.1.0 using Forte cc.) Copied entire EMBASSY directory from 1.12.0 EMBOSS to 2.1.0. Tried gmake in EMNU 1.0.4. BOOM, it couldn't find X11 symbols. Tossed that, installed new 1.0.5 distribution clean in embassy directory. In EMNU did ./configure (or ./configure --with-x, same phenotype) gmake boom, it couldn't find X11 symbols again. After dropping into the source directory it was doing: /bin/sh ../libtool --mode=link gcc -O -o emnu emnu.o ../../../plplot/libplplot.la ../../../ajax/libajax.la ../../../nucleus/libnucleus.la -lmenu -lform -lmenu -lform -lsocket -lm -lnsl -lncurses which you'll notice has no -lX11 on the end, and of course it couldn't link in the X11 bits. So I ran this manually with -lX11 added to the end and it worked. I just checked, emnu under 1.12.0 still will gmake. Why is it that in EMBOSS 1.12.0 EMNU knows to use the X11 lib but has forgotten to do so in 2.1.0??? Thanks, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From mathog at mendel.bio.caltech.edu Thu Jan 3 15:29:24 2002 From: mathog at mendel.bio.caltech.edu (David Mathog) Date: Thu, 03 Jan 2002 12:29:24 -0800 Subject: 2.1.0 build glitches on Solaris 8 Message-ID: > The --with-png really should be --with-pngdriver=directory > Assuming you have libpng* in /foo/bar/lib then 'directory' should > be /foo/bar (the /lib is assumed to be essential). If the > configure can find the libpng, libz and libgd libraries in a > standard place it will automatically include png support. Standard > places are generally /usr/lib and /usr/local/lib But why does --with-png work when configure has CC=gcc and fail when CC=cc? For what it's worth, libpng and libgd are in /usr/local and libz is in /usr/lib where some Solaris package installed it. > > If you don't specify a directory then the default value of --with-png > is "yes" hence the problem (at least that is what I suspect). > > If your gd,z & png are not all in a standard place If there really was a unix "standard" we wouldn't be using configure in the first place. gd may never ship with any unix distribution but over time more and more Unix's will come with both libz and libpng, and since manufacturers tend to put what they ship in /usr/lib, the "standard place" over time will most likely shift from /usr/local/lib to /usr/lib. > As for the varargs messages. That is a fairly well known problem > with some installations of gcc on Solaris. It is a difficult one > for the configure scripts to resolve satisfactorily. The easiest > dirty hack would be to edit ajax/Makefile and delete all > occurrences of '-I/usr/include' since then there will be no > conflicts between the standard and GNU varargs headers. That's what I had to do with sim4 which had the opposite problem - it was picking up conflicting definitions. Here no definition is being found. David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From ableasby at hgmp.mrc.ac.uk Thu Jan 3 15:47:48 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Thu, 3 Jan 2002 20:47:48 GMT Subject: 2.1.0 build glitches on Solaris 8 Message-ID: <200201032047.UAA23623@bromine.hgmp.mrc.ac.uk> "But why does --with-png work when configure has CC=gcc and fail when CC=cc? For what it's worth, libpng and libgd are in /usr/local and libz is in /usr/lib where some Solaris package installed it." Possibly because the 'cc' never looks in /usr/local whereas gcc well might. >If there really was a unix "standard" we wouldn't be using configure Indeed, but we could argue unnecessarily about that until the cows come home and still not be able to second-guess various perversities. Its either choose something reasonably standard or ordered otherwise its a separate --with-gd=x --with-z=y --with=png=z or a find / -name "libpng*" -exec etc :-) >From what you describe of the locations on your system then both compilers 'might' work if you specify --with-pngdriver=/usr/local btw: Maybe emboss-bug is the best list for all this sort of thing. Cheers Alan From milius at mail.ahc.umn.edu Thu Jan 3 19:04:45 2002 From: milius at mail.ahc.umn.edu (Bob Milius) Date: Thu, 3 Jan 2002 18:04:45 -0600 (CST) Subject: emboss and mac osx 10.1 Message-ID: Hello, I just tried to configure/make emboss 2.1 on an iBook running Mac OSX 10.1 The build proceeds for a while and then ends with the following error: rm -fr .libs/libplplot.la .libs/libplplot.* .libs/libplplot.* cc -dynamiclib -undefined suppress -o .libs/libplplot.4.0.99.dylib pdfutils.lo plargs.lo plbox.lo plcont.lo plcore.lo plctrl.lo plcvt.lo pldtik.lo plfill.lo plhist.lo plline.lo plmap.lo plot3d.lo plpage.lo plsdef.lo plshade.lo plsym.lo pltick.lo plvpor.lo plwind.lo plstripc.lo dg300.lo hpgl.lo impress.lo linuxvga.lo ljiip.lo ljii.lo next.lo null.lo pbm.lo plbuf.lo plmeta.lo ps.lo tek.lo xfig.lo xwin.lo gdpng.lo -lc -install_name /usr/local/lib/libplplot.4.dylib -compatibility_version 5 -current_version 5.99 ld: -undefined error must be used when -twolevel_namespace is in effect /usr/bin/libtool: internal link edit command failed make[2]: *** [libplplot.la] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all-recursive] Error 1 I tried putting "setenv LDFLAGS -flat_namespace" in my ~/.cshrc file, but doesn't seem to help. any advice will be appreciated. thanks, -bob -- ------------------------------------------------------------------------------ Robert Milius, PhD 612-624-3993 (voice) Center for Computational Genomics and Bioinformatics 612-626-6069 (fax) University of Minnesota milius at umn.edu ------------------------------------------------------------------------------ "I have never in my life learned anything from any man who agreed with me." - Dudley Field Malone (1882-1950) American Diplomat, Lawyer ------------------------------------------------------------------------------ From ableasby at hgmp.mrc.ac.uk Thu Jan 3 19:12:28 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Fri, 4 Jan 2002 00:12:28 GMT Subject: emboss and mac osx 10.1 Message-ID: <200201040012.AAA00510@bromine.hgmp.mrc.ac.uk> That's known. Apple expressed an interest in EMBOSS but would not provide a machine. As we don't have one we cannot officially support MacOSX. Nevertheless, if anyone wants to contact me personally about this we can perhaps take it from there. Alan From jackl at cmbi.kun.nl Fri Jan 4 07:48:18 2002 From: jackl at cmbi.kun.nl (Jack Leunissen) Date: Fri, 4 Jan 2002 13:48:18 +0100 Subject: 2.1.0 build glitches on Solaris 8 References: <200201032047.UAA23623@bromine.hgmp.mrc.ac.uk> Message-ID: <002a01c1951f$8acb7940$0400a8c0@dalicon.com> Hi David and Alan, > >From what you describe of the locations on your system then both > compilers 'might' work if you specify --with-pngdriver=/usr/local Not only 'might'. Installing "png" in /usr/local, and putting an up-to-date version of "gd" in the same location was all that I needed do on Solaris 8. And of course specify the "--with-pngdriver=/usr/local" ... regards, Jack From maojn at yahoo.com Mon Jan 7 14:35:53 2002 From: maojn at yahoo.com (Jean Mao) Date: Mon, 7 Jan 2002 14:35:53 -0500 Subject: what's the difference in latest release to previous one? Message-ID: <00f501c197b2$877ccb00$cc8a70a5@citjmao> hi, could someone tell me where i can find the file that contains the difference between the latest version of Emboss and previous version? thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20020107/f56c45e1/attachment.html From ableasby at hgmp.mrc.ac.uk Fri Jan 11 20:11:27 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Sat, 12 Jan 2002 01:11:27 GMT Subject: EMBOSS 2.2.0 released Message-ID: <200201120111.BAA29642@bromine.hgmp.mrc.ac.uk> EMBOSS 2.2.0 has several additional programs in the protein structure area. Contacts, Dichet, Psiblasts, Scopalign, Siggen and Sigscan are now made by default. A small utility, Biosed, has also been added to allow simple deletion or replacement of subsequences or residues. Documentation for some other new programs (e.g. Alignwrap) is being prepared. Routines to allow EMBOSS to read sequences from the latest SRS servers has been incorporated in this release. Bugfixes: Sequential access of GenBank flatfiles is again possible. Problems with alignment reports have been fixed. est2genome now works with unindexed sequence files. Other minor fixes and changes have been incorporated. Alan From sgmd at genetik.fu-berlin.de Mon Jan 14 05:53:52 2002 From: sgmd at genetik.fu-berlin.de (Thomas Siegmund) Date: Mon, 14 Jan 2002 11:53:52 +0100 Subject: Announce: X / KDE GUI for EMBOSS V0.6 Message-ID: <20020114105244.2640C17A78@mercury.hgmp.mrc.ac.uk> Hello everybody, I'd like to let you know that I have relased version 0.6 of EMBOSS.kaptn, a X11 and KDE2 based GUI for EMBOSS. The new release covers 120 applications with (almost) all features. Given the speed of the EMBOSS developers the GUI probably will never be complete, but it's getting close. Highlights of this release are support for primer3 (Thanks for putting this in EMBOSS!) and for the output formats in various apps. Version 0.6 of EMBOSS.kaptn is available at http://userpage.fu-berlin.de/~sgmd . >From the ChangeLog: Version 0.6 - aformat option for needle.kaptn, merger.kaptn, matcher.kaptn, water.kaptn - rformat option for antigenic.kaptn, dan.kaptn, diffseq.kaptn, digest.kaptn, garnier.kaptn, helixturnhelix.kaptn, restrict.kaptn, sigcleave.kaptn - new: stretcher.kaptn, seqmatchall.kaptn, supermatcher.kaptn, rebaseextract.kaptn, biosed.kaptn - Better desktop integration: install script can put EMBOSS submenu into the K desktop menu. - small fixes in codcmp.kaptn, emowse.kaptn, dreg.kaptn, preg.kaptn, showseq.kaptn - shrinked some more windows Version 0.59 - new: prima, primersearch, primer3 With best regards Thomas -- Thomas Siegmund Freie Universit?t Berlin Institut f?r Genetik Arnimallee 7 14195 Berlin Germany Tel: +49 30 838 54868 Fax: +49 30 838 54395 http://userpage.fu-berlin.de/~sgmd From ableasby at hgmp.mrc.ac.uk Mon Jan 14 10:19:05 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Mon, 14 Jan 2002 15:19:05 GMT Subject: EMBOSS 2.2.0 patchfiles Message-ID: <200201141519.PAA11675@bromine.hgmp.mrc.ac.uk> A couple of minor bugs have been noticed in 2.2.0 One is that on some alignment reports the gap and similarity scores are transposed. The other is a case sensitivity in patmatdb. There are fixes for both problems in the ftp://ftp.uk.embnet.org/pub/EMBOSS/patchfiles/ directory. Just replace the existing ajax/ajalign.c and emboss/patmatdb.c files with the new ones and recompile. Alan From cwtsai73 at yahoo.com.tw Mon Jan 14 21:34:50 2002 From: cwtsai73 at yahoo.com.tw (momo) Date: Tue, 15 Jan 2002 10:34:50 +0800 Subject: general announcements and discussions by end users Message-ID: general announcements and discussions by end users -------------------------------------------------------------------- Chien-Wei Tsai Bioinformatics Center of National Yang-Ming University Tel : (02) 28267000 ext 5666 ; 886922343950 Email : cwtsai73 at yahoo.com.tw -------------------------------------------------------------------- ?(???????*.???{&???(??]??,j?m????????h??& From david.lapointe at umassmed.edu Tue Jan 15 08:16:48 2002 From: david.lapointe at umassmed.edu (David) Date: Tue, 15 Jan 2002 08:16:48 -0500 Subject: EMBOSS 2.2.0 released References: <200201120111.BAA29642@bromine.hgmp.mrc.ac.uk> Message-ID: <3C442BC0.EBB86514@umassmed.edu> Alan, Two of these programs (Dichet,psiblasts) also have no documentation. Are these being prepared? David ableasby at hgmp.mrc.ac.uk wrote: > > EMBOSS 2.2.0 has several additional programs in the protein structure > area. Contacts, Dichet, Psiblasts, Scopalign, Siggen and Sigscan are > now made by default. A small utility, Biosed, has also been added to > allow simple deletion or replacement of subsequences or > residues. Documentation for some other new programs (e.g. Alignwrap) > is being prepared. > > Routines to allow EMBOSS to read sequences from the latest SRS > servers has been incorporated in this release. > > Bugfixes: Sequential access of GenBank flatfiles is again possible. > Problems with alignment reports have been fixed. est2genome now > works with unindexed sequence files. Other minor fixes and changes > have been incorporated. > > Alan -- .david David Lapointe "Ein gutes Paradigma ist ein Schatz fur Leben," Max Delbruck From gwilliam at hgmp.mrc.ac.uk Tue Jan 15 08:23:23 2002 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Tue, 15 Jan 2002 13:23:23 +0000 Subject: EMBOSS 2.2.0 released References: <200201120111.BAA29642@bromine.hgmp.mrc.ac.uk> <3C442BC0.EBB86514@umassmed.edu> Message-ID: <3C442D4A.C870B001@hgmp.mrc.ac.uk> I'm doing documentation for alignwrap, dichet, psiblasts, swissparse. Gary David wrote: > > Alan, > > Two of these programs (Dichet,psiblasts) also have no documentation. Are > these being prepared? > > David > > ableasby at hgmp.mrc.ac.uk wrote: > > > > EMBOSS 2.2.0 has several additional programs in the protein structure > > area. Contacts, Dichet, Psiblasts, Scopalign, Siggen and Sigscan are > > now made by default. A small utility, Biosed, has also been added to > > allow simple deletion or replacement of subsequences or > > residues. Documentation for some other new programs (e.g. Alignwrap) > > is being prepared. > > > > Routines to allow EMBOSS to read sequences from the latest SRS > > servers has been incorporated in this release. > > > > Bugfixes: Sequential access of GenBank flatfiles is again possible. > > Problems with alignment reports have been fixed. est2genome now > > works with unindexed sequence files. Other minor fixes and changes > > have been incorporated. > > > > Alan > > -- > .david > David Lapointe > "Ein gutes Paradigma ist ein Schatz fur Leben," Max Delbruck -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From p.ernst at dkfz-heidelberg.de Tue Jan 15 11:56:29 2002 From: p.ernst at dkfz-heidelberg.de (Peter Ernst) Date: Tue, 15 Jan 2002 17:56:29 +0100 (MET) Subject: Announcement: Patch 4.02 for W2H-4.0 released Message-ID: W2H-EMBOSS patch announcement (patch 4.02) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ (W2H is a free WWW interface to sequence analysis software tools like EMBOSS) contains: w2h/ACDParser.pm w2h/acd.y w2h/emboss/util.appdesc_from_wossname w2h/emboss/util.appmenu_from_wossname Files acd.y and ACDParser.pm: ============================== This patch for W2H supports the new keywords in EMBOSS' .acd files, that came with EMBOSS-2.1.0 (e.g. gui, report, align, section, ...). Furthermore, the behavior of W2H has changed if the application has two input sequence qualifiers (e.g. water, needle, est2genome): W2H allows the selection of both input sequences from the main window. If you don't want the new behavior for some EMBOSS applications, you can specify a list of application names, where W2H should continue to use the old scheme. E.g. Est2Genome seems to work better with the old scheme. Just add the following variable in your Cfg.pl(.emboss) file: # --- comma separated list of applications where W2H should NOT convert # SeqSet and SeqAll parameters into Sequence parameters # (affects the cases: 1 sequence vs. many sequences or # many sequences vs. many sequences $EMBOSS_KEEP_SEQSETS = "Est2Genome"; Files emboss/util.appmenu_from_wossname and emboss/util.appdesc_from_wossname: ============================================ The new versions of the utilities (used to create config/application.menu.emboss # menu structure see Cfg.pl's $APPMENU config/application.desc.emboss # appl.descriptions see Cfg.pl's $APPDESCRIPTION ) can create slightly improved versions of the configuration files from the EMBOSS application wossname: util.appmenu_from_wossname: creates a menu structure with several sub-levels (ignoring applications which are not "GUIable" (gui:N), e.g. emnu) util.appdesc_from_wossname [ maxlen-of-desc-text(70) ]: this version can cut the description texts to a specified length (defaults to 70 chars). With a value of "0" the description texts provided by wossname are not cut (old behavior). Availability: ftp://genome.dkfz-heidelberg.de/pub/w2h and/or ftp://ftp.ebi.ac.uk/pub/software/unix/w2h W2H homepage: http://www.w2h.dkfz-heidelberg.de/ and/or http://industry.ebi.ac.uk/w2h 15 January 2002 Peter Ernst From haruna at sgi.com Thu Jan 17 19:55:44 2002 From: haruna at sgi.com (Haruna Cofer) Date: Thu, 17 Jan 2002 19:55:44 -0500 Subject: EMBOSS on SGI Message-ID: <3C477290.A8031A6D@sgi.com> Hi there -- Just FYI, my porting notes for EMBOSS 2.2.0 on SGI systems is available from here: http://www.sgi.com/solutions/sciences/chembio/resources/emboss/ I would like to have these changes incorporated automatically in the distribution, but I can tell it's going to take me a little while to figure out how to do that. In the meantime, please do let me know if you have any questions or problems. Thanks! -- Haruna Cofer @ SGI From d.m.a.martin at dundee.ac.uk Fri Jan 18 04:21:51 2002 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Fri, 18 Jan 2002 09:21:51 -0000 (GMT) Subject: EMBOSS on SGI In-Reply-To: <3C477290.A8031A6D@sgi.com> References: <3C477290.A8031A6D@sgi.com> Message-ID: <49617.134.36.67.217.1011345711.squirrel@www.bioinformatics.dundee.ac.uk> > Hi there -- > > Just FYI, my porting notes for EMBOSS 2.2.0 on SGI systems is available > from here: > > http://www.sgi.com/solutions/sciences/chembio/resources/emboss/ I'll add the link in to the admin guide. One comment.. On the porting tips you mention editing a particular file but neglect to say which file one is supposed to be editing.. > I would like to have these changes incorporated automatically in the > distribution, but I can tell it's going to take me a little while to > figure out how to do that. In the meantime, please do let me know if > you have any questions or problems. Thanks! Possibly the best thing is to build a freeware package that will then require the relevant dependencies? ...d > > -- Haruna Cofer @ SGI -- David Martin PhD Bioinformatics Scientific Officer Molecular Interactions and Post Genomics Centre University of Dundee From ableasby at hgmp.mrc.ac.uk Fri Jan 18 10:33:52 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Fri, 18 Jan 2002 15:33:52 GMT Subject: EMBOSS on SGI Message-ID: <200201181533.PAA03918@bromine.hgmp.mrc.ac.uk> >Possibly the best thing is to build a freeware package that will then >require the relevant dependencies? I disagree. The best thing is for it all to be in the standard configure rather than having lots of different out-of-sync EMBOSS versions out there. That's why I pointed Huruna in the direction of the relevant tools (and added health warnings of course). It does need to be done by someone with access to the machines involved ... otherwise we'd have done it already. Cheers Alan From haruna at sgi.com Fri Jan 18 12:02:44 2002 From: haruna at sgi.com (Haruna Cofer) Date: Fri, 18 Jan 2002 12:02:44 -0500 Subject: EMBOSS on SGI References: <3C477290.A8031A6D@sgi.com> <49617.134.36.67.217.1011345711.squirrel@www.bioinformatics.dundee.ac.uk> Message-ID: <3C485534.81C4E69E@sgi.com> David Martin wrote: > > One comment.. On the porting tips you mention editing a particular file but > neglect to say which file one is supposed to be editing.. Oops, Thanks, David! I'll fix that! -- Haruna :) -- Haruna N. Cofer SGI ChemPharm Applications From cutler at tularik.com Fri Jan 18 20:41:40 2002 From: cutler at tularik.com (Gene Cutler) Date: Fri, 18 Jan 2002 17:41:40 -0800 Subject: Bug in seqret Message-ID: I have just upgraded to version 2.2.0 of EMBOSS, and have found some not nice behavior in the seqret program. If I try to retrieve a list of sequences, and there is a sequence which is not in the database, it will die. This is less nice than the previous version which would quit, and less nice yet than the optimal behavior of printing out an error message and continuing on to the next sequence. My questions are: Have other observed this? Are there plans to fix this? Where is the source code that this is occurring in so that I can try to fix it myself? Thanks. From cutler at tularik.com Mon Jan 21 14:16:17 2002 From: cutler at tularik.com (Gene Cutler) Date: Mon, 21 Jan 2002 11:16:17 -0800 Subject: Using method: app for seq retrieval Message-ID: <57EC1F62-0EA3-11D6-9F5B-0030657E760C@tularik.com> I'm trying to follow the docs for using a custom app for sequence retrieval. I made a test perl script which just prints out a fasta sequence to stdout, but I can't get the retrieval to work. In my emboss config, I've put this: DB test [ method: app format: fasta app: "/usr/local/bin/test.pl %s" type: N ] and then typed: seqret test:XYZ but I get: Error: Unable to read sequence 'test:XYZ' If I run "/usr/local/bin/test.pl XYZ" from the command line, it prints out the fasta sequence properly. I also tried this: DB test [ methodsingle: app format: fasta app: "/usr/local/bin/test.pl %s" type: N ] but that's even worse: Error: Bad database attribute 'methodsingle' Reads and writes (returns) sequences Error: No access method for database 'test' Error: no access method available for 'test:XYZ' Error: Unable to read sequence 'test:XYZ' I am using EMBOSS version 2.2.0 From karbak at cmu.edu Tue Jan 22 01:01:17 2002 From: karbak at cmu.edu (K. Arun) Date: 22 Jan 2002 01:01:17 -0500 Subject: redata/rebaseextract bug ? Message-ID: <87k7uagc0i.fsf@epsilon.bio.cmu.edu> Hello, I recently compiled EMBOSS 2.2.0 (with the patched files mentioned earlier on this list) on a Debian Linux machine, and have been using it (mostly) without problems for a few days now. I encountered an interesting anomaly this evening while indexing and checking REBASE release 201. ------------ $ redata EcoRI Search REBASE for enzyme name, references, suppliers etc. Output file [outfile.redata]: stdout EcoRI Recognition site is ESCHERICHIACOLIRY leaving sticky ends Cut positions 5':0 3':0 [5':0 3':0] Organism: G^AATTC Methylated: R.N. Yoshimori Source: 3(6) -snip- ------------ (organism and recognition site are interchanged) I've been having other problems with 'restrict', but this one seems to require fixing first. Am I doing something wrong ? I extracted REBASE 201 (the withrefm.201 file) with rebaseextract as indicated in the documentation. Thanks, -arun -- arun krishnaswamy biological sciences, mellon institute, carnegie mellon university PGP: 0x5606B2B1 GPG: 1024D/C75FD05C From ableasby at hgmp.mrc.ac.uk Tue Jan 22 02:40:22 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 22 Jan 2002 07:40:22 GMT Subject: redata/rebaseextract bug ? Message-ID: <200201220740.HAA05738@bromine.hgmp.mrc.ac.uk> Hi, This isn't a bug. You have been using rebaseextract on the withref.201 file. You should be using the withrefm.201 file. Alan From simon.andrews at bbsrc.ac.uk Tue Jan 22 03:20:09 2002 From: simon.andrews at bbsrc.ac.uk (simon andrews (BI)) Date: Tue, 22 Jan 2002 08:20:09 -0000 Subject: Using method: app for seq retrieval Message-ID: <2DC41140A89ED411989D00508BDCD9EDEA5246@bi-exsrv1.iapc.bbsrc.ac.uk> > -----Original Message----- > From: Gene Cutler [mailto:cutler at tularik.com] > Sent: Monday, January 21, 2002 7:16 PM > To: emboss at embnet.org > Subject: Using method: app for seq retrieval > > > I'm trying to follow the docs for using a custom > app for sequence retrieval. > I made a test perl script which just prints out a > fasta sequence to stdout, but I can't get the retrieval > to work. In my emboss config, I've put > this: > > DB test [ > method: app > format: fasta > app: "/usr/local/bin/test.pl %s" > type: N > ] Gene, I've done this successfully, using the following entry in emboss.default, where allmus is a perl script which returns a fasta file. DB allmus [ type: N method: app format: fasta app: "/usr/users/andrewss/bin/allmus" comment: "Farm of all Mouse Genomic seqs" ] The database and sequence name will automatically be passed to the script with this setup. They will be passed in the form "database:accession". Since I've made my script pretty generic, I use the following snippet to extract the accession code from what is passed to the script; my ($reference) = @ARGV; if ($reference =~ /:(.+)$/){ $reference = $1; } else { die "\n*** ERROR *** Couldn't get accession after : from $reference\n\n"; } You just then need to use $reference to find your sequence and print it to STDOUT. I seem to also remember that you have to have the accession number requested at the start of the fasta header, otherwise you get an error saying the file could not be found. So if you ask for "seqret script:cheese" You have to return a file looking like: >cheese ..... AGCTAGC... and not >chalk .... ATCGCTA otherwise seqret will curl up and die. Hope this helps Simon. ---- Simon Andrews PhD Bioinformatics Dept The Babraham Institute simon.andrews at bbsrc.ac.uk +44 (0)1223 496463 From karbak at cmu.edu Tue Jan 22 03:36:43 2002 From: karbak at cmu.edu (K. Arun) Date: 22 Jan 2002 03:36:43 -0500 Subject: redata/rebaseextract bug ? In-Reply-To: <200201220740.HAA05738@bromine.hgmp.mrc.ac.uk> ('s message of "Tue, 22 Jan 2002 07:40:22 GMT") References: <200201220740.HAA05738@bromine.hgmp.mrc.ac.uk> Message-ID: <87adv6g4tg.fsf@epsilon.bio.cmu.edu> >>>>> "ableasby" == writes: ableasby> Hi, This isn't a bug. You have been using rebaseextract on ableasby> the withref.201 file. You should be using the withrefm.201 ableasby> file. That worked. I knew I'd made a mistake somewhere. Thanks, -arun -- arun krishnaswamy biological sciences, mellon institute, carnegie mellon university PGP: 0x5606B2B1 GPG: 1024D/C75FD05C From peter.rice at uk.lionbioscience.com Tue Jan 22 04:54:24 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Tue, 22 Jan 2002 09:54:24 +0000 Subject: Using method: app for seq retrieval References: <57EC1F62-0EA3-11D6-9F5B-0030657E760C@tularik.com> Message-ID: <3C4D36D0.623CD24E@uk.lionbioscience.com> Gene Cutler wrote: > In my emboss config, I've put > this: > > DB test [ > method: app > format: fasta > app: "/usr/local/bin/test.pl %s" > type: N > ] > > and then typed: > seqret test:XYZ > > but I get: > Error: Unable to read sequence 'test:XYZ' > > If I run "/usr/local/bin/test.pl XYZ" from the command line, it prints > out > the fasta sequence properly. The definition looks right to me. As a check, can seqret read the fasta file that it writes (in case it has bad characters). Seqret will check the sequence ID from the fasta format is 'XYZ'. It does this because you are passing this as a database USA (test:XYZ) so it acts like a database search and tests the 'id'. I think this is the most likely cause. You can add a few "print STDERR" lines to your perl script to check it is being executed, and what happens. You can also try seqret with -debug on the command line to get a seqret.dbg file that should help trace the problem. >I also tried this: >DB test [ > methodsingle: app > format: fasta > app: "/usr/local/bin/test.pl %s" > type: N >] > >but that's even worse: >Error: Bad database attribute 'methodsingle' methodentry, not methodsingle. Was this an error in the documentation somewhere, or just a bad guess? regards, Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From glatting at dkfz-heidelberg.de Fri Jan 25 04:04:20 2002 From: glatting at dkfz-heidelberg.de (Karl-Heinz Glatting) Date: Fri, 25 Jan 2002 10:04:20 +0100 (MET) Subject: bug in reading GCG databases Message-ID: Dear all, There is probably a bug in reading GCG formatted databases via EMBOSS when using expressions like swissprot:* (other wildcard specifications and extracting entries by name or so do work). The first sequence is read properly but afterwards everything is out of sync. I wrote a small emboss application which does nothing more than ajAcdGetSeqall and a loop over ajSeqallNext. I found the problem also when using applications like fuzzpro or water. I fixed this by deleting line 1994 ajFileGets (qryd->libs, &line); in routine seqGcgReadSeq in ajseqdb.c and it seems to work now but because I don't understand what this line was good for :-) I'am not sure whether it will work in all possible cases. BTW, is it true that subsections do not work for GCG formatted databases? When I define a database like Pir1 as an example and use pir1:* I get the whole PIR database. best regards, Karl-Heinz Karl-Heinz Glatting Bioinformatics Service Group Department of Molecular Biophysics Deutsches Krebsforschungszentrum (DKFZ) (German Cancer Research Center) Heidelberg, Germany E-Mail: glatting at dkfz-heidelberg.de From lefranc at ligm.igh.cnrs.fr Wed Jan 2 15:28:19 2002 From: lefranc at ligm.igh.cnrs.fr (Marie-Paule Lefranc) Date: Wed, 02 Jan 2002 16:28:19 +0100 Subject: New IMGT tools freely available at http://imgt.cines.fr Message-ID: <5.1.0.14.1.20020102161051.009f6830@ligm.igh.cnrs.fr> Dear Colleague, I will be grateful if you accepted to diffuse this accompanying announcement so that your members be aware of this new development of IMGT. With many thanks for your help. Best Regards Yours sincerely Marie-Paule Lefranc -------------- next part -------------- A non-text attachment was scrubbed... Name: IMGT news Dec 2001.doc Type: application/msword Size: 28672 bytes Desc: not available URL: -------------- next part -------------- IMGT, the international ImMunoGeneTics database http://imgt.cines.fr LIGM, IGH, UPR CNRS 1142 141 rue de la Cardonille 34396 Montpellier Cedex 5 FRANCE Tel: +33 (0)4 99 61 99 65 Fax: +33 (0)4 99 61 99 01 From lefranc at ligm.igh.cnrs.fr Wed Jan 2 15:28:19 2002 From: lefranc at ligm.igh.cnrs.fr (Marie-Paule Lefranc) Date: Wed, 02 Jan 2002 16:28:19 +0100 Subject: New IMGT tools freely available at http://imgt.cines.fr Message-ID: <5.1.0.14.1.20020102161051.009f6830@ligm.igh.cnrs.fr> Dear Colleague, I will be grateful if you accepted to diffuse this accompanying announcement so that your members be aware of this new development of IMGT. With many thanks for your help. Best Regards Yours sincerely Marie-Paule Lefranc -------------- next part -------------- A non-text attachment was scrubbed... Name: IMGT news Dec 2001.doc Type: application/msword Size: 28672 bytes Desc: not available URL: -------------- next part -------------- IMGT, the international ImMunoGeneTics database http://imgt.cines.fr LIGM, IGH, UPR CNRS 1142 141 rue de la Cardonille 34396 Montpellier Cedex 5 FRANCE Tel: +33 (0)4 99 61 99 65 Fax: +33 (0)4 99 61 99 01 From mathog at mendel.bio.caltech.edu Thu Jan 3 19:07:25 2002 From: mathog at mendel.bio.caltech.edu (David Mathog) Date: Thu, 03 Jan 2002 11:07:25 -0800 Subject: 2.1.0 build glitches on Solaris 8 Message-ID: I just tried installing 2.1.0 on Solaris 8. After unpacking it in the top level did: # ./configure --with-png # make and it blew up in the libtool link of plplot complaining about not finding "yes/lib". Turns out plplot/Makefile had CPPFLAGS = -Iyes/include -Iyes LDFLAGS = -Lyes/lib which is seriously wrong. Tried again with gmake and had the same problem. Oops, just realized that make clean doesn't remove Makefile. Take them all out with: # find . -name Makefile -exec rm {} \; # ./configure --with-png and this time plplot/Makefile shows: CPPFLAGS = -I/usr/include -I/usr LDFLAGS = -L/usr/lib and now make for plplot works. Bizarre - some sort of first run initialization problem exists. Unfortunately all is still not working right.. When it hits ajacd.o it blows up with: ajacd.c: In function `acdBadVal': ajacd.c:2827: `__builtin_va_alist' undeclared (first use in this function) ajacd.c:2827: (Each undeclared identifier is reported only once ajacd.c:2827: for each function it appears in.) ajacd.c: In function `acdLog': ajacd.c:13323: `__builtin_va_alist' undeclared (first use in this function) ajacd.c: In function `acdPretty': ajacd.c:13359: `__builtin_va_alist' undeclared (first use in this function) *** Error code 1 make: Fatal error: Command failed for target `ajacd.lo' Current working directory /usr/local/src/EMBOSS-2.1.0/ajax *** Error code 1 make: Fatal error: Command failed for target `all-recursive' This was using gcc version 2.95.3 20010315 (release). I've seen problems with that builtin before, but usually it's the other way around - conflicting definitions when gcc uses certain includes. Here it looks like those includes were left out. Try once more using the native (Forte) compiler (which is how I built the 1.12.0 version) # make clean # find . -name Makefile -exec rm {} \; # export CC=cc # echo $CC cc # ./configure --with-png RATS - it rejects the png stuff this time with: checking if png driver is wanted... yes checking for inflateEnd in -lz... yes checking for png_destroy_read_struct in -lpng... no No png driver will be made due to librarys missing/old. continue on anyway to see if this resolves the builtin problem... Yes, apparently using the Forte compiler takes care of the va_builtin problem - at the cost of losing the PNG device. The Forte compiler is: Sun WorkShop 6 update 1 C 5.2 2000/09/11 Somebody must have this working on Solaris. What is the magic incantation to get a full build with PNG enabled??? Thanks, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From ableasby at hgmp.mrc.ac.uk Thu Jan 3 20:05:01 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Thu, 3 Jan 2002 20:05:01 GMT Subject: 2.1.0 build glitches on Solaris 8 Message-ID: <200201032005.UAA20974@bromine.hgmp.mrc.ac.uk> The --with-png really should be --with-pngdriver=directory Assuming you have libpng* in /foo/bar/lib then 'directory' should be /foo/bar (the /lib is assumed to be essential). If the configure can find the libpng, libz and libgd libraries in a standard place it will automatically include png support. Standard places are generally /usr/lib and /usr/local/lib If you don't specify a directory then the default value of --with-png is "yes" hence the problem (at least that is what I suspect). If your gd,z & png are not all in a standard place then it may help to put them all in the same lib directory somewhere. The command ./configure --help is useful for the syntax. As for the varargs messages. That is a fairly well known problem with some installations of gcc on Solaris. It is a difficult one for the configure scripts to resolve satisfactorily. The easiest dirty hack would be to edit ajax/Makefile and delete all occurrences of '-I/usr/include' since then there will be no conflicts between the standard and GNU varargs headers. Alan From mathog at mendel.bio.caltech.edu Thu Jan 3 20:18:19 2002 From: mathog at mendel.bio.caltech.edu (David Mathog) Date: Thu, 03 Jan 2002 12:18:19 -0800 Subject: EMNU build under EMBOSS 2.1.0 Message-ID: Trying to get EMBASSY bits working under EMBOSS 2.1.0 on Solaris 8 (following mostly successful build of EMBOSS 2.1.0 using Forte cc.) Copied entire EMBASSY directory from 1.12.0 EMBOSS to 2.1.0. Tried gmake in EMNU 1.0.4. BOOM, it couldn't find X11 symbols. Tossed that, installed new 1.0.5 distribution clean in embassy directory. In EMNU did ./configure (or ./configure --with-x, same phenotype) gmake boom, it couldn't find X11 symbols again. After dropping into the source directory it was doing: /bin/sh ../libtool --mode=link gcc -O -o emnu emnu.o ../../../plplot/libplplot.la ../../../ajax/libajax.la ../../../nucleus/libnucleus.la -lmenu -lform -lmenu -lform -lsocket -lm -lnsl -lncurses which you'll notice has no -lX11 on the end, and of course it couldn't link in the X11 bits. So I ran this manually with -lX11 added to the end and it worked. I just checked, emnu under 1.12.0 still will gmake. Why is it that in EMBOSS 1.12.0 EMNU knows to use the X11 lib but has forgotten to do so in 2.1.0??? Thanks, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From mathog at mendel.bio.caltech.edu Thu Jan 3 20:29:24 2002 From: mathog at mendel.bio.caltech.edu (David Mathog) Date: Thu, 03 Jan 2002 12:29:24 -0800 Subject: 2.1.0 build glitches on Solaris 8 Message-ID: > The --with-png really should be --with-pngdriver=directory > Assuming you have libpng* in /foo/bar/lib then 'directory' should > be /foo/bar (the /lib is assumed to be essential). If the > configure can find the libpng, libz and libgd libraries in a > standard place it will automatically include png support. Standard > places are generally /usr/lib and /usr/local/lib But why does --with-png work when configure has CC=gcc and fail when CC=cc? For what it's worth, libpng and libgd are in /usr/local and libz is in /usr/lib where some Solaris package installed it. > > If you don't specify a directory then the default value of --with-png > is "yes" hence the problem (at least that is what I suspect). > > If your gd,z & png are not all in a standard place If there really was a unix "standard" we wouldn't be using configure in the first place. gd may never ship with any unix distribution but over time more and more Unix's will come with both libz and libpng, and since manufacturers tend to put what they ship in /usr/lib, the "standard place" over time will most likely shift from /usr/local/lib to /usr/lib. > As for the varargs messages. That is a fairly well known problem > with some installations of gcc on Solaris. It is a difficult one > for the configure scripts to resolve satisfactorily. The easiest > dirty hack would be to edit ajax/Makefile and delete all > occurrences of '-I/usr/include' since then there will be no > conflicts between the standard and GNU varargs headers. That's what I had to do with sim4 which had the opposite problem - it was picking up conflicting definitions. Here no definition is being found. David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From ableasby at hgmp.mrc.ac.uk Thu Jan 3 20:47:48 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Thu, 3 Jan 2002 20:47:48 GMT Subject: 2.1.0 build glitches on Solaris 8 Message-ID: <200201032047.UAA23623@bromine.hgmp.mrc.ac.uk> "But why does --with-png work when configure has CC=gcc and fail when CC=cc? For what it's worth, libpng and libgd are in /usr/local and libz is in /usr/lib where some Solaris package installed it." Possibly because the 'cc' never looks in /usr/local whereas gcc well might. >If there really was a unix "standard" we wouldn't be using configure Indeed, but we could argue unnecessarily about that until the cows come home and still not be able to second-guess various perversities. Its either choose something reasonably standard or ordered otherwise its a separate --with-gd=x --with-z=y --with=png=z or a find / -name "libpng*" -exec etc :-) >From what you describe of the locations on your system then both compilers 'might' work if you specify --with-pngdriver=/usr/local btw: Maybe emboss-bug is the best list for all this sort of thing. Cheers Alan From milius at mail.ahc.umn.edu Fri Jan 4 00:04:45 2002 From: milius at mail.ahc.umn.edu (Bob Milius) Date: Thu, 3 Jan 2002 18:04:45 -0600 (CST) Subject: emboss and mac osx 10.1 Message-ID: Hello, I just tried to configure/make emboss 2.1 on an iBook running Mac OSX 10.1 The build proceeds for a while and then ends with the following error: rm -fr .libs/libplplot.la .libs/libplplot.* .libs/libplplot.* cc -dynamiclib -undefined suppress -o .libs/libplplot.4.0.99.dylib pdfutils.lo plargs.lo plbox.lo plcont.lo plcore.lo plctrl.lo plcvt.lo pldtik.lo plfill.lo plhist.lo plline.lo plmap.lo plot3d.lo plpage.lo plsdef.lo plshade.lo plsym.lo pltick.lo plvpor.lo plwind.lo plstripc.lo dg300.lo hpgl.lo impress.lo linuxvga.lo ljiip.lo ljii.lo next.lo null.lo pbm.lo plbuf.lo plmeta.lo ps.lo tek.lo xfig.lo xwin.lo gdpng.lo -lc -install_name /usr/local/lib/libplplot.4.dylib -compatibility_version 5 -current_version 5.99 ld: -undefined error must be used when -twolevel_namespace is in effect /usr/bin/libtool: internal link edit command failed make[2]: *** [libplplot.la] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all-recursive] Error 1 I tried putting "setenv LDFLAGS -flat_namespace" in my ~/.cshrc file, but doesn't seem to help. any advice will be appreciated. thanks, -bob -- ------------------------------------------------------------------------------ Robert Milius, PhD 612-624-3993 (voice) Center for Computational Genomics and Bioinformatics 612-626-6069 (fax) University of Minnesota milius at umn.edu ------------------------------------------------------------------------------ "I have never in my life learned anything from any man who agreed with me." - Dudley Field Malone (1882-1950) American Diplomat, Lawyer ------------------------------------------------------------------------------ From ableasby at hgmp.mrc.ac.uk Fri Jan 4 00:12:28 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Fri, 4 Jan 2002 00:12:28 GMT Subject: emboss and mac osx 10.1 Message-ID: <200201040012.AAA00510@bromine.hgmp.mrc.ac.uk> That's known. Apple expressed an interest in EMBOSS but would not provide a machine. As we don't have one we cannot officially support MacOSX. Nevertheless, if anyone wants to contact me personally about this we can perhaps take it from there. Alan From jackl at cmbi.kun.nl Fri Jan 4 12:48:18 2002 From: jackl at cmbi.kun.nl (Jack Leunissen) Date: Fri, 4 Jan 2002 13:48:18 +0100 Subject: 2.1.0 build glitches on Solaris 8 References: <200201032047.UAA23623@bromine.hgmp.mrc.ac.uk> Message-ID: <002a01c1951f$8acb7940$0400a8c0@dalicon.com> Hi David and Alan, > >From what you describe of the locations on your system then both > compilers 'might' work if you specify --with-pngdriver=/usr/local Not only 'might'. Installing "png" in /usr/local, and putting an up-to-date version of "gd" in the same location was all that I needed do on Solaris 8. And of course specify the "--with-pngdriver=/usr/local" ... regards, Jack From maojn at yahoo.com Mon Jan 7 19:35:53 2002 From: maojn at yahoo.com (Jean Mao) Date: Mon, 7 Jan 2002 14:35:53 -0500 Subject: what's the difference in latest release to previous one? Message-ID: <00f501c197b2$877ccb00$cc8a70a5@citjmao> hi, could someone tell me where i can find the file that contains the difference between the latest version of Emboss and previous version? thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From ableasby at hgmp.mrc.ac.uk Sat Jan 12 01:11:27 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Sat, 12 Jan 2002 01:11:27 GMT Subject: EMBOSS 2.2.0 released Message-ID: <200201120111.BAA29642@bromine.hgmp.mrc.ac.uk> EMBOSS 2.2.0 has several additional programs in the protein structure area. Contacts, Dichet, Psiblasts, Scopalign, Siggen and Sigscan are now made by default. A small utility, Biosed, has also been added to allow simple deletion or replacement of subsequences or residues. Documentation for some other new programs (e.g. Alignwrap) is being prepared. Routines to allow EMBOSS to read sequences from the latest SRS servers has been incorporated in this release. Bugfixes: Sequential access of GenBank flatfiles is again possible. Problems with alignment reports have been fixed. est2genome now works with unindexed sequence files. Other minor fixes and changes have been incorporated. Alan From sgmd at genetik.fu-berlin.de Mon Jan 14 10:53:52 2002 From: sgmd at genetik.fu-berlin.de (Thomas Siegmund) Date: Mon, 14 Jan 2002 11:53:52 +0100 Subject: Announce: X / KDE GUI for EMBOSS V0.6 Message-ID: <20020114105244.2640C17A78@mercury.hgmp.mrc.ac.uk> Hello everybody, I'd like to let you know that I have relased version 0.6 of EMBOSS.kaptn, a X11 and KDE2 based GUI for EMBOSS. The new release covers 120 applications with (almost) all features. Given the speed of the EMBOSS developers the GUI probably will never be complete, but it's getting close. Highlights of this release are support for primer3 (Thanks for putting this in EMBOSS!) and for the output formats in various apps. Version 0.6 of EMBOSS.kaptn is available at http://userpage.fu-berlin.de/~sgmd . >From the ChangeLog: Version 0.6 - aformat option for needle.kaptn, merger.kaptn, matcher.kaptn, water.kaptn - rformat option for antigenic.kaptn, dan.kaptn, diffseq.kaptn, digest.kaptn, garnier.kaptn, helixturnhelix.kaptn, restrict.kaptn, sigcleave.kaptn - new: stretcher.kaptn, seqmatchall.kaptn, supermatcher.kaptn, rebaseextract.kaptn, biosed.kaptn - Better desktop integration: install script can put EMBOSS submenu into the K desktop menu. - small fixes in codcmp.kaptn, emowse.kaptn, dreg.kaptn, preg.kaptn, showseq.kaptn - shrinked some more windows Version 0.59 - new: prima, primersearch, primer3 With best regards Thomas -- Thomas Siegmund Freie Universit?t Berlin Institut f?r Genetik Arnimallee 7 14195 Berlin Germany Tel: +49 30 838 54868 Fax: +49 30 838 54395 http://userpage.fu-berlin.de/~sgmd From ableasby at hgmp.mrc.ac.uk Mon Jan 14 15:19:05 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Mon, 14 Jan 2002 15:19:05 GMT Subject: EMBOSS 2.2.0 patchfiles Message-ID: <200201141519.PAA11675@bromine.hgmp.mrc.ac.uk> A couple of minor bugs have been noticed in 2.2.0 One is that on some alignment reports the gap and similarity scores are transposed. The other is a case sensitivity in patmatdb. There are fixes for both problems in the ftp://ftp.uk.embnet.org/pub/EMBOSS/patchfiles/ directory. Just replace the existing ajax/ajalign.c and emboss/patmatdb.c files with the new ones and recompile. Alan From cwtsai73 at yahoo.com.tw Tue Jan 15 02:34:50 2002 From: cwtsai73 at yahoo.com.tw (momo) Date: Tue, 15 Jan 2002 10:34:50 +0800 Subject: general announcements and discussions by end users Message-ID: general announcements and discussions by end users -------------------------------------------------------------------- Chien-Wei Tsai Bioinformatics Center of National Yang-Ming University Tel : (02) 28267000 ext 5666 ; 886922343950 Email : cwtsai73 at yahoo.com.tw -------------------------------------------------------------------- ?(???????*.???{&???(??]??,j?m????????h??& From david.lapointe at umassmed.edu Tue Jan 15 13:16:48 2002 From: david.lapointe at umassmed.edu (David) Date: Tue, 15 Jan 2002 08:16:48 -0500 Subject: EMBOSS 2.2.0 released References: <200201120111.BAA29642@bromine.hgmp.mrc.ac.uk> Message-ID: <3C442BC0.EBB86514@umassmed.edu> Alan, Two of these programs (Dichet,psiblasts) also have no documentation. Are these being prepared? David ableasby at hgmp.mrc.ac.uk wrote: > > EMBOSS 2.2.0 has several additional programs in the protein structure > area. Contacts, Dichet, Psiblasts, Scopalign, Siggen and Sigscan are > now made by default. A small utility, Biosed, has also been added to > allow simple deletion or replacement of subsequences or > residues. Documentation for some other new programs (e.g. Alignwrap) > is being prepared. > > Routines to allow EMBOSS to read sequences from the latest SRS > servers has been incorporated in this release. > > Bugfixes: Sequential access of GenBank flatfiles is again possible. > Problems with alignment reports have been fixed. est2genome now > works with unindexed sequence files. Other minor fixes and changes > have been incorporated. > > Alan -- .david David Lapointe "Ein gutes Paradigma ist ein Schatz fur Leben," Max Delbruck From gwilliam at hgmp.mrc.ac.uk Tue Jan 15 13:23:23 2002 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Tue, 15 Jan 2002 13:23:23 +0000 Subject: EMBOSS 2.2.0 released References: <200201120111.BAA29642@bromine.hgmp.mrc.ac.uk> <3C442BC0.EBB86514@umassmed.edu> Message-ID: <3C442D4A.C870B001@hgmp.mrc.ac.uk> I'm doing documentation for alignwrap, dichet, psiblasts, swissparse. Gary David wrote: > > Alan, > > Two of these programs (Dichet,psiblasts) also have no documentation. Are > these being prepared? > > David > > ableasby at hgmp.mrc.ac.uk wrote: > > > > EMBOSS 2.2.0 has several additional programs in the protein structure > > area. Contacts, Dichet, Psiblasts, Scopalign, Siggen and Sigscan are > > now made by default. A small utility, Biosed, has also been added to > > allow simple deletion or replacement of subsequences or > > residues. Documentation for some other new programs (e.g. Alignwrap) > > is being prepared. > > > > Routines to allow EMBOSS to read sequences from the latest SRS > > servers has been incorporated in this release. > > > > Bugfixes: Sequential access of GenBank flatfiles is again possible. > > Problems with alignment reports have been fixed. est2genome now > > works with unindexed sequence files. Other minor fixes and changes > > have been incorporated. > > > > Alan > > -- > .david > David Lapointe > "Ein gutes Paradigma ist ein Schatz fur Leben," Max Delbruck -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From p.ernst at dkfz-heidelberg.de Tue Jan 15 16:56:29 2002 From: p.ernst at dkfz-heidelberg.de (Peter Ernst) Date: Tue, 15 Jan 2002 17:56:29 +0100 (MET) Subject: Announcement: Patch 4.02 for W2H-4.0 released Message-ID: W2H-EMBOSS patch announcement (patch 4.02) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ (W2H is a free WWW interface to sequence analysis software tools like EMBOSS) contains: w2h/ACDParser.pm w2h/acd.y w2h/emboss/util.appdesc_from_wossname w2h/emboss/util.appmenu_from_wossname Files acd.y and ACDParser.pm: ============================== This patch for W2H supports the new keywords in EMBOSS' .acd files, that came with EMBOSS-2.1.0 (e.g. gui, report, align, section, ...). Furthermore, the behavior of W2H has changed if the application has two input sequence qualifiers (e.g. water, needle, est2genome): W2H allows the selection of both input sequences from the main window. If you don't want the new behavior for some EMBOSS applications, you can specify a list of application names, where W2H should continue to use the old scheme. E.g. Est2Genome seems to work better with the old scheme. Just add the following variable in your Cfg.pl(.emboss) file: # --- comma separated list of applications where W2H should NOT convert # SeqSet and SeqAll parameters into Sequence parameters # (affects the cases: 1 sequence vs. many sequences or # many sequences vs. many sequences $EMBOSS_KEEP_SEQSETS = "Est2Genome"; Files emboss/util.appmenu_from_wossname and emboss/util.appdesc_from_wossname: ============================================ The new versions of the utilities (used to create config/application.menu.emboss # menu structure see Cfg.pl's $APPMENU config/application.desc.emboss # appl.descriptions see Cfg.pl's $APPDESCRIPTION ) can create slightly improved versions of the configuration files from the EMBOSS application wossname: util.appmenu_from_wossname: creates a menu structure with several sub-levels (ignoring applications which are not "GUIable" (gui:N), e.g. emnu) util.appdesc_from_wossname [ maxlen-of-desc-text(70) ]: this version can cut the description texts to a specified length (defaults to 70 chars). With a value of "0" the description texts provided by wossname are not cut (old behavior). Availability: ftp://genome.dkfz-heidelberg.de/pub/w2h and/or ftp://ftp.ebi.ac.uk/pub/software/unix/w2h W2H homepage: http://www.w2h.dkfz-heidelberg.de/ and/or http://industry.ebi.ac.uk/w2h 15 January 2002 Peter Ernst From haruna at sgi.com Fri Jan 18 00:55:44 2002 From: haruna at sgi.com (Haruna Cofer) Date: Thu, 17 Jan 2002 19:55:44 -0500 Subject: EMBOSS on SGI Message-ID: <3C477290.A8031A6D@sgi.com> Hi there -- Just FYI, my porting notes for EMBOSS 2.2.0 on SGI systems is available from here: http://www.sgi.com/solutions/sciences/chembio/resources/emboss/ I would like to have these changes incorporated automatically in the distribution, but I can tell it's going to take me a little while to figure out how to do that. In the meantime, please do let me know if you have any questions or problems. Thanks! -- Haruna Cofer @ SGI From d.m.a.martin at dundee.ac.uk Fri Jan 18 09:21:51 2002 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Fri, 18 Jan 2002 09:21:51 -0000 (GMT) Subject: EMBOSS on SGI In-Reply-To: <3C477290.A8031A6D@sgi.com> References: <3C477290.A8031A6D@sgi.com> Message-ID: <49617.134.36.67.217.1011345711.squirrel@www.bioinformatics.dundee.ac.uk> > Hi there -- > > Just FYI, my porting notes for EMBOSS 2.2.0 on SGI systems is available > from here: > > http://www.sgi.com/solutions/sciences/chembio/resources/emboss/ I'll add the link in to the admin guide. One comment.. On the porting tips you mention editing a particular file but neglect to say which file one is supposed to be editing.. > I would like to have these changes incorporated automatically in the > distribution, but I can tell it's going to take me a little while to > figure out how to do that. In the meantime, please do let me know if > you have any questions or problems. Thanks! Possibly the best thing is to build a freeware package that will then require the relevant dependencies? ...d > > -- Haruna Cofer @ SGI -- David Martin PhD Bioinformatics Scientific Officer Molecular Interactions and Post Genomics Centre University of Dundee From ableasby at hgmp.mrc.ac.uk Fri Jan 18 15:33:52 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Fri, 18 Jan 2002 15:33:52 GMT Subject: EMBOSS on SGI Message-ID: <200201181533.PAA03918@bromine.hgmp.mrc.ac.uk> >Possibly the best thing is to build a freeware package that will then >require the relevant dependencies? I disagree. The best thing is for it all to be in the standard configure rather than having lots of different out-of-sync EMBOSS versions out there. That's why I pointed Huruna in the direction of the relevant tools (and added health warnings of course). It does need to be done by someone with access to the machines involved ... otherwise we'd have done it already. Cheers Alan From haruna at sgi.com Fri Jan 18 17:02:44 2002 From: haruna at sgi.com (Haruna Cofer) Date: Fri, 18 Jan 2002 12:02:44 -0500 Subject: EMBOSS on SGI References: <3C477290.A8031A6D@sgi.com> <49617.134.36.67.217.1011345711.squirrel@www.bioinformatics.dundee.ac.uk> Message-ID: <3C485534.81C4E69E@sgi.com> David Martin wrote: > > One comment.. On the porting tips you mention editing a particular file but > neglect to say which file one is supposed to be editing.. Oops, Thanks, David! I'll fix that! -- Haruna :) -- Haruna N. Cofer SGI ChemPharm Applications From cutler at tularik.com Sat Jan 19 01:41:40 2002 From: cutler at tularik.com (Gene Cutler) Date: Fri, 18 Jan 2002 17:41:40 -0800 Subject: Bug in seqret Message-ID: I have just upgraded to version 2.2.0 of EMBOSS, and have found some not nice behavior in the seqret program. If I try to retrieve a list of sequences, and there is a sequence which is not in the database, it will die. This is less nice than the previous version which would quit, and less nice yet than the optimal behavior of printing out an error message and continuing on to the next sequence. My questions are: Have other observed this? Are there plans to fix this? Where is the source code that this is occurring in so that I can try to fix it myself? Thanks. From cutler at tularik.com Mon Jan 21 19:16:17 2002 From: cutler at tularik.com (Gene Cutler) Date: Mon, 21 Jan 2002 11:16:17 -0800 Subject: Using method: app for seq retrieval Message-ID: <57EC1F62-0EA3-11D6-9F5B-0030657E760C@tularik.com> I'm trying to follow the docs for using a custom app for sequence retrieval. I made a test perl script which just prints out a fasta sequence to stdout, but I can't get the retrieval to work. In my emboss config, I've put this: DB test [ method: app format: fasta app: "/usr/local/bin/test.pl %s" type: N ] and then typed: seqret test:XYZ but I get: Error: Unable to read sequence 'test:XYZ' If I run "/usr/local/bin/test.pl XYZ" from the command line, it prints out the fasta sequence properly. I also tried this: DB test [ methodsingle: app format: fasta app: "/usr/local/bin/test.pl %s" type: N ] but that's even worse: Error: Bad database attribute 'methodsingle' Reads and writes (returns) sequences Error: No access method for database 'test' Error: no access method available for 'test:XYZ' Error: Unable to read sequence 'test:XYZ' I am using EMBOSS version 2.2.0 From karbak at cmu.edu Tue Jan 22 06:01:17 2002 From: karbak at cmu.edu (K. Arun) Date: 22 Jan 2002 01:01:17 -0500 Subject: redata/rebaseextract bug ? Message-ID: <87k7uagc0i.fsf@epsilon.bio.cmu.edu> Hello, I recently compiled EMBOSS 2.2.0 (with the patched files mentioned earlier on this list) on a Debian Linux machine, and have been using it (mostly) without problems for a few days now. I encountered an interesting anomaly this evening while indexing and checking REBASE release 201. ------------ $ redata EcoRI Search REBASE for enzyme name, references, suppliers etc. Output file [outfile.redata]: stdout EcoRI Recognition site is ESCHERICHIACOLIRY leaving sticky ends Cut positions 5':0 3':0 [5':0 3':0] Organism: G^AATTC Methylated: R.N. Yoshimori Source: 3(6) -snip- ------------ (organism and recognition site are interchanged) I've been having other problems with 'restrict', but this one seems to require fixing first. Am I doing something wrong ? I extracted REBASE 201 (the withrefm.201 file) with rebaseextract as indicated in the documentation. Thanks, -arun -- arun krishnaswamy biological sciences, mellon institute, carnegie mellon university PGP: 0x5606B2B1 GPG: 1024D/C75FD05C From ableasby at hgmp.mrc.ac.uk Tue Jan 22 07:40:22 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 22 Jan 2002 07:40:22 GMT Subject: redata/rebaseextract bug ? Message-ID: <200201220740.HAA05738@bromine.hgmp.mrc.ac.uk> Hi, This isn't a bug. You have been using rebaseextract on the withref.201 file. You should be using the withrefm.201 file. Alan From simon.andrews at bbsrc.ac.uk Tue Jan 22 08:20:09 2002 From: simon.andrews at bbsrc.ac.uk (simon andrews (BI)) Date: Tue, 22 Jan 2002 08:20:09 -0000 Subject: Using method: app for seq retrieval Message-ID: <2DC41140A89ED411989D00508BDCD9EDEA5246@bi-exsrv1.iapc.bbsrc.ac.uk> > -----Original Message----- > From: Gene Cutler [mailto:cutler at tularik.com] > Sent: Monday, January 21, 2002 7:16 PM > To: emboss at embnet.org > Subject: Using method: app for seq retrieval > > > I'm trying to follow the docs for using a custom > app for sequence retrieval. > I made a test perl script which just prints out a > fasta sequence to stdout, but I can't get the retrieval > to work. In my emboss config, I've put > this: > > DB test [ > method: app > format: fasta > app: "/usr/local/bin/test.pl %s" > type: N > ] Gene, I've done this successfully, using the following entry in emboss.default, where allmus is a perl script which returns a fasta file. DB allmus [ type: N method: app format: fasta app: "/usr/users/andrewss/bin/allmus" comment: "Farm of all Mouse Genomic seqs" ] The database and sequence name will automatically be passed to the script with this setup. They will be passed in the form "database:accession". Since I've made my script pretty generic, I use the following snippet to extract the accession code from what is passed to the script; my ($reference) = @ARGV; if ($reference =~ /:(.+)$/){ $reference = $1; } else { die "\n*** ERROR *** Couldn't get accession after : from $reference\n\n"; } You just then need to use $reference to find your sequence and print it to STDOUT. I seem to also remember that you have to have the accession number requested at the start of the fasta header, otherwise you get an error saying the file could not be found. So if you ask for "seqret script:cheese" You have to return a file looking like: >cheese ..... AGCTAGC... and not >chalk .... ATCGCTA otherwise seqret will curl up and die. Hope this helps Simon. ---- Simon Andrews PhD Bioinformatics Dept The Babraham Institute simon.andrews at bbsrc.ac.uk +44 (0)1223 496463 From karbak at cmu.edu Tue Jan 22 08:36:43 2002 From: karbak at cmu.edu (K. Arun) Date: 22 Jan 2002 03:36:43 -0500 Subject: redata/rebaseextract bug ? In-Reply-To: <200201220740.HAA05738@bromine.hgmp.mrc.ac.uk> ('s message of "Tue, 22 Jan 2002 07:40:22 GMT") References: <200201220740.HAA05738@bromine.hgmp.mrc.ac.uk> Message-ID: <87adv6g4tg.fsf@epsilon.bio.cmu.edu> >>>>> "ableasby" == writes: ableasby> Hi, This isn't a bug. You have been using rebaseextract on ableasby> the withref.201 file. You should be using the withrefm.201 ableasby> file. That worked. I knew I'd made a mistake somewhere. Thanks, -arun -- arun krishnaswamy biological sciences, mellon institute, carnegie mellon university PGP: 0x5606B2B1 GPG: 1024D/C75FD05C From peter.rice at uk.lionbioscience.com Tue Jan 22 09:54:24 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Tue, 22 Jan 2002 09:54:24 +0000 Subject: Using method: app for seq retrieval References: <57EC1F62-0EA3-11D6-9F5B-0030657E760C@tularik.com> Message-ID: <3C4D36D0.623CD24E@uk.lionbioscience.com> Gene Cutler wrote: > In my emboss config, I've put > this: > > DB test [ > method: app > format: fasta > app: "/usr/local/bin/test.pl %s" > type: N > ] > > and then typed: > seqret test:XYZ > > but I get: > Error: Unable to read sequence 'test:XYZ' > > If I run "/usr/local/bin/test.pl XYZ" from the command line, it prints > out > the fasta sequence properly. The definition looks right to me. As a check, can seqret read the fasta file that it writes (in case it has bad characters). Seqret will check the sequence ID from the fasta format is 'XYZ'. It does this because you are passing this as a database USA (test:XYZ) so it acts like a database search and tests the 'id'. I think this is the most likely cause. You can add a few "print STDERR" lines to your perl script to check it is being executed, and what happens. You can also try seqret with -debug on the command line to get a seqret.dbg file that should help trace the problem. >I also tried this: >DB test [ > methodsingle: app > format: fasta > app: "/usr/local/bin/test.pl %s" > type: N >] > >but that's even worse: >Error: Bad database attribute 'methodsingle' methodentry, not methodsingle. Was this an error in the documentation somewhere, or just a bad guess? regards, Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From glatting at dkfz-heidelberg.de Fri Jan 25 09:04:20 2002 From: glatting at dkfz-heidelberg.de (Karl-Heinz Glatting) Date: Fri, 25 Jan 2002 10:04:20 +0100 (MET) Subject: bug in reading GCG databases Message-ID: Dear all, There is probably a bug in reading GCG formatted databases via EMBOSS when using expressions like swissprot:* (other wildcard specifications and extracting entries by name or so do work). The first sequence is read properly but afterwards everything is out of sync. I wrote a small emboss application which does nothing more than ajAcdGetSeqall and a loop over ajSeqallNext. I found the problem also when using applications like fuzzpro or water. I fixed this by deleting line 1994 ajFileGets (qryd->libs, &line); in routine seqGcgReadSeq in ajseqdb.c and it seems to work now but because I don't understand what this line was good for :-) I'am not sure whether it will work in all possible cases. BTW, is it true that subsections do not work for GCG formatted databases? When I define a database like Pir1 as an example and use pir1:* I get the whole PIR database. best regards, Karl-Heinz Karl-Heinz Glatting Bioinformatics Service Group Department of Molecular Biophysics Deutsches Krebsforschungszentrum (DKFZ) (German Cancer Research Center) Heidelberg, Germany E-Mail: glatting at dkfz-heidelberg.de