Bioinformatic packages for Red Hat Linux 9 and Fedora Linux

Why bother?

Having noticed sometimes — not always, to be honest

I eventually decided to do something about it[1]. The situation is a big enough nuisance for us computer nerds and we might still tolerate it, because we are used to put up with such nonsense, but it only spells trouble for poor biologists who are just trying to get their job done — obtaining a grant or winning that Nobel Prize.

Okay, where's the beef?

Below you will find a number of packages ready to be installed on a Red Hat 9 system. Click on a name to obtain more information on the package: licensing, homepage, a more verbose description, a change log of the packaging (not of the actual tool) and a list of the files comprising it.

You might notice that not all of them were packaged by me — I am including those anyway, to keep the repository as comprehensive as possible. This is still largely in progress: I am working to improve what is available now and to add more packages in the near future. Feel free to get in touch with me with suggestions or comments.

Signatures

All packages have been digitally signed with my GnuPG key. In its default configuration, RPM will print an annoying yet harmless warning that includes the text V3 DSA signature: NOKEY, key ID 1d284fa2, meaning that the package has been signed with a key that is not trusted (yet). You could ignore the message; you could configure or tell RPM not to check keys at all, but a better idea is to have my key recognised. It only takes a few seconds.

First you need to obtain my public key. It is available from the very same server that hosts this page or through public key servers like http://pgp.mit.edu/ or http://www.keyserver.net/ (just search for my name or email address). Please get in touch with me if you still don't trust any of those sources, so that we can make different arrangements.

Once you have the public key saved or pasted to a file, issue as root the command

rpm --import filename

That's it! Now you can verify a package, prior to installation, with the command

rpm --checksig packagename

(you might want to try it before and after my key has been imported, to see the two different outputs)

Sources

Packages that I build are also available in source form. This might be useful if you intend to customise the packages or attempt to rebuild them with different options or for another distribution — whatever the reason, good luck.

The last column will provide a link whenever a source RPM is available. Please notice that, to avoid confusion, for groups of packages built from the same source package, the link is present only once, in the entry for the main binary package. E.g., EMBOSS2, libEMBOSS2 and libEMBOSS2-devel are built from just one source package, which is linked only from the EMBOSS2 row.

Source packages can be used in two ways. If you only want to attempt a rebuild, without leaving files behind, issue the command

rpmbuild --rebuild packagename.src.rpm

If the attempt is successful, your binary package or packages will be in the directory /usr/src/redhat/RPMS/i386 (or i586, i686 and so on... check the last twenty lines or so in RPM's output).

Otherwise, you can install a source package, leaving the files around until you remove them. Issuing the command

rpm -Uvh packagename.src.rpm

the package spec file will be installed in /usr/src/redhat/SPECS, while any source archives and patches will be copied to /usr/src/redhat/SOURCES. To rebuild the package, issue

The above assumes you are issuing the commands as root. It is usually recommended to build packages as a regular user instead. Patrick Ben Koetter provides a brief, yet excellent explanation of the procedure.

rpmbuild -bb /usr/src/redhat/SPECS/packagename.spec

while the command

rpmbuild --rmsource --rmspec /usr/src/redhat/SPECS/packagename.spec

will remove the spec file and all source archives and patches associated with it. Any customisations to the packages should be done by editing the spec file, adding patches and so on.

[1]The idea for the whole silly blurb above came much later.

Name Summary Version—release Date Size Binary
EMBOSS The European Molecular Biology Open Software Suite 2.8.0—0.fdr.2 2004-01-18 6.7M i386 Source
A somewhat improved configuration file is available. It defines methods to retrieve sequences from the GenBank and GenPept databases online, through the Canadian EMBNET server, rather than using a local database. Copy to /etc/emboss.default after having installed the EMBOSS and libEMBOSS packages. Eventually it is going to be merged into the EMBOSS package.
EMBOSS-GUI Web frontend for EMBOSS 1.0—0.fdr.4 2004-01-18 44K noarch Source
Web frontend for EMBOSS. Requires a web server and the perl-MailTools package below
Jemboss GUI to EMBOSS 2.8.0—0.fdr.2 2004-01-18 3.9M i386
artemis DNA sequence viewer and annotation tool 5—0.br.3 2003-09-25 4.2M noarch Source
clustalw Multiple Sequence Alignment Program 1.83—0.fdr.5 2004-01-18 168K i386 Source
gbrowse Generic genome browser 1.58—0.fdr.4 2004-01-18 260K i386 Source
gbrowse-frontend gbrowse 1.58—0.fdr.4 2004-01-18 924K i386
gd A graphics library for quick creation of PNG or JPEG images. 2.0.15—1 2004-01-18 188K i386 Source
GD library version 2, backported from Fedora Core 1. Requires by perl-GD 2, which is in turn required by GBrowse and Bioperl. Only install on Red Hat Linux 9 and only by using rpm -i rather than rpm -U.
gd-devel The development libraries and header files for gd. 2.0.15—1 2004-01-18 72K i386
gd-progs Utility programs that use libgd. 2.0.15—1 2004-01-18 24K i386
gibbs Gibbs motif sampler 9.95—1.icc 2003-04-03 380K i686
Version from the biolinux.org site, compiled with Intel's compiler for highest performance. It hasn't been linked statically, thus it requires the package with Intel's libraries (intel-credist below).
gridengine Distributed resource management software 5.3p5—0.fdr.1 2004-01-25 4.6M i386 Source
Work in progress. Known to be broken.
gridengine Distributed resource management software 5.3p5—0.fdr.2 2004-01-26 4.6M i386
Work in progress. Known to be broken.
gridengine Distributed resource management software 5.3p5—0.fdr.3 2004-01-27 4.6M i386 Source
Work in progress. Known to be broken.
gridengine-devel Distributed resource management software 5.3p5—0.fdr.1 2004-01-25 124K i386
gridengine-devel Distributed resource management software 5.3p5—0.fdr.2 2004-01-26 124K i386
gridengine-devel Distributed resource management software 5.3p5—0.fdr.3 2004-01-27 124K i386
gridengine-examples Distributed resource management software 5.3p5—0.fdr.3 2004-01-27 16K i386
gridengine-execd Grid Engine node daemon 5.3p5—0.fdr.3 2004-01-27 8.0K i386
gridengine-qmaster Grid Engine master daemon 5.3p5—0.fdr.3 2004-01-27 8.0K i386
hmmer Sequence analysis using profile hidden Markov Models 2.3.1—1static 2003-06-14 3.6M i686
Version from the official site, compiled with Intel's compiler for highest performance. Linked statically, so that it doesn't require the package with Intel's libraries.
intel-credist Intel(R) C/C++ redistributable files 7.0—1 2002-11-27 460K i386
Only needed by the gibbs package at the moment.
jalview A Java multiple alignment editor 1.8—0.br.4 2003-09-25 324K noarch Source
libEMBOSS2 Main library for EMBOSS 2.8.0—0.fdr.2 2004-01-18 1.9M i386
Required by the EMBOSS package.
libEMBOSS2-devel Development header files for EMBOSS 2.8.0—0.fdr.2 2004-01-18 728K i386
ncbi-blast NCBI BLAST server suite 2.2.6—0.fdr.3 2004-01-18 16M i386 Source
perl-AcePerl Perl extension for object-oriented access to ACEDB Databases 1.86—0.fdr.4 2004-01-18 352K i386 Source
perl-Algorithm-Diff Compute 'intelligent' differences between two files / lists 1.15—0.fdr.4 2004-01-18 36K noarch Source
perl-Bioperl Perl tools for bioinformatics, genomics and life science research 1.4—0.fdr.2 2004-01-18 3.0M noarch Source
perl-Bioperl-Corba-Client bioperl-corba-client Perl module 0.20040119—0.fdr.1 2004-01-20 40K noarch Source
perl-Bioperl-Corba-Server bioperl-corba-server Perl module 0.2—0.fdr.1 2004-01-18 60K noarch Source
perl-Bioperl-DB Bioperl-DB Perl module 1.1.0—0.fdr.2 2004-01-20 172K noarch Source
perl-Bioperl-Run Perl tools for bioinformatics, genomics and life science research 1.4—0.fdr.1 2004-01-18 1.8M noarch Source
perl-CORBA-ORBit CORBA-ORBit Perl module 0.4.7—0.fdr.1 2004-01-18 588K i386 Source
perl-Cache-Cache Cache-Cache Perl module 1.02—0.fdr.1 2004-01-18 80K noarch Source
perl-Clone Clone Perl module 0.15—0.fdr.1 2004-01-18 56K i386 Source
perl-Data-Stag Perl extension for structured tags 0.03—0.fdr.4 2004-01-18 112K noarch Source
perl-Enum C style enumerated types and bitmask flags in Perl 1.016—0.br.4 2004-01-18 16K noarch Source
perl-Error Error Perl module 0.15—0.fdr.1 2004-01-20 16K noarch Source
perl-GD Perl interface to GD Graphics Library 2.11—0.fdr.2 2004-01-18 224K i386 Source
perl-GD-SVG GD-SVG Perl module 0.24—0.fdr.1 2004-01-18 44K noarch Source
perl-GDTextUtil GDTextUtil Perl module 0.86—0.fdr.1 2004-01-18 32K noarch Source
perl-Graph Perl extension for graph operations 0.20101—0.fdr.4 2004-01-18 44K noarch Source
perl-Heap Perl extensions for keeping data partially sorted 0.50—0.br.4 2004-01-18 48K noarch Source
perl-IO-String Emulate IO::File interface for in-core strings 1.02—0.fdr.3 2004-01-18 12K noarch Source
perl-IO-stringy Perl extension for I/O on in-core objects like strings and arrays 2.108—0.br.4 2004-01-18 104K noarch Source
perl-IPC-ShareLite IPC-ShareLite Perl module 0.09—0.fdr.1 2004-01-18 76K i386 Source
perl-MIME-Lite Low-calorie MIME generator 3.01_02—0.fdr.5 2004-01-18 84K noarch Source
perl-MailTools MailTools module for Perl 1.59—0.br.2 2004-01-18 88K noarch Source
perl-Math-Derivative Math-Derivative Perl module 0.01—0.fdr.1 2004-01-18 8.0K noarch Source
perl-Math-Spline Math-Spline Perl module 0.01—0.fdr.1 2004-01-18 8.0K noarch Source
perl-SOAP-Lite Perl extension for client and server side SOAP implementation 0.55—0.br.5 2004-01-18 184K noarch Source
perl-SOAP-Lite-JABBER Net::Jabber support for SOAP::Lite 0.55—0.br.5 2004-01-18 12K noarch
perl-SOAP-Lite-MQ MQ transport support for SOAP::Lite (SOAP::Transport::MQ) 0.55—0.br.5 2004-01-18 8.0K noarch
perl-SOAP-Lite-examples SOAP::Lite - examples 0.55—0.br.5 2004-01-18 68K noarch
perl-SVG SVG Perl module 2.28—0.fdr.1 2004-01-18 64K noarch Source
perl-SVG-Graph SVG-Graph Perl module 0.01—0.fdr.1 2004-01-18 64K noarch Source
perl-Statistics-Descriptive Statistics-Descriptive Perl module 2.6—0.fdr.1 2004-01-18 20K noarch Source
perl-Text-Shellwords Perl extension to parse lines into tokens like the shell does 1.02—0.fdr.5 2004-01-18 8.0K noarch Source
perl-Tk Perl Tk module 800.025—0.fdr.3 2004-01-18 9.4M i386 Source
perl-Tk-demos-800.025-0.br.2.i386.rpm: not—an 0 manifest):
perl-Tk-demos perl-Tk demos 800.025—0.fdr.3 2004-01-18 236K i386
perl-Tree-DAG_Node Tree-DAG_Node Perl module 1.04—0.fdr.1 2004-01-18 56K noarch Source
perl-XML-Writer Perl extension for writing XML documents. 0.4—0.br.4 2004-01-18 20K noarch Source
perl-blastGraphic blastGraphic Perl module 0.01—0.fdr.1 2004-01-18 56K noarch Source
pfaat Protein Family Alignment Annotation Tool 1.0—0.br.2 2003-10-02 2.1M noarch Source
rocks-sge Sun Grid Engine 5.3p5—1 2004-01-12 496K i386 Source
rocks-sge-devel Grid Engine development 5.3p4—3 2004-01-11 124K i386
rocks-sge-execd SGE Execution Host extensions 5.3p5—1 2004-01-12 8.0K i386
rocks-sge-qmaster SGE QMaster extensions 5.3p5—1 2004-01-12 8.0K i386
sgeblast sgeblast is web frontend for blast with gridengine as backend DRM 0.2—1 2002-11-23 12K i386
A version of the wwwblast frontend that submits jobs to a GridEngine cluster.
sim4 Aligns an expressed DNA sequence with a genomic sequence 20030921—0.fdr.3 2004-01-18 64K i386 Source
2005-02-07 1.4M
wwwblast Standalone WWW BLAST server suite Apr.21.2003—0.fdr.3 2004-01-18 11M i386 Source
A web frontend for NCBI's BLAST server suite. Requires a web server such as Apache to be installed.

Last modified: 2005-02-07 16:30:29 EST. All feedback to Rudi Chiarito <nutello@sweetness.com>.