Biopackages.net

1
Biopackages.net

• Operating System Packages for Bioinformatics
• Allen Day
• 2005.05.17

2
What is a package?

• Software, config files, documentation, and/or
  data encapsulated in a single file
• Metadata describing
• Version, license, package category
• Dependencies
• What the package provides

3

• GMOD target audience
• Small MODs

4
Package Dependency Graph

• Dependencies
• What the package provides

chado-Hsa
genome-Hsa-annotation-gene
genome-Hsa-annotation-affymetrix
postgresql-AffxSeq
chado
perl-bioperl
perl-go-perl
genome-Hsa-nib
ucsc-blat
postgresql-server
obo-core
5
Dependencies

• Build Dependency
• Installation Dependency

6
What is a Package Manager?

• Tools to manage installation, upgrade,
  uninstallation of packages
• Verify package integrity (checksums)
• Maintain system integrity
• Transactional
• Allow rollbacks
• Dependency checking
• Dependency graph recursion
• Allow software customization (patches)

7
Current Generation of PMs

• RPM
• Dpkg
• Apt
• Yum
• Emerge
• tgz/bz2
• Windows Installer

8
Why bioinformatics packages?

• Consistency of installation process
• Bioinfo. package installs vary wildly, and
  commonly lack documentation
• Automatic dependency installation
• Perl modules especially bad bioperl has 60
  modules in its dependency tree
• Integrity/Auditing of system state
• Know an installed package works, which version,
  how to replicate system setup
• Tighter integration with operating system
• Daemons, config log file locations, etc.

9
Whats available?

• RPM packages only right now
• Primary focus on Fedora Core 2
• Some RPMs also available for
• Fedora Core 3
• RedHat 9
• Cygwin

10
Whats available?

• Three primary foci
• Applications
• Libraries
• Data sets

11
Applications

• Gbrowse
• Textpresso
• BLAT daemon
• NCBI Toolkit (BLAST, etc)
• HMMer

12
Whats available?

• Libraries
• Bioperl
• R Bioconductor
• Squid
• EMBOSS

13
Whats available?

• Data sets
• Genome protein sequence
• Sequence features
• Ontologies
• All installed using a common directory structure

14
Whats available?

• UCSC tools (utilities, BLAT system service, CGI
  scripts)
• Bioperl
• R / Bioconductor
• GMOD apps (Gbrowse, Textpresso, )
• Data packages
• Genome sequence (fa, nib, blastdb)
• Genome features (Affy probeset alignments, mRNA,
  etc)

15
GMOD Components Available
gmod-web-Hsa
chado-Hsa
gbrowse
textpresso
turnkey
chado

• Hsa can be substituted for your organism
• Currently built for Cel, Hsa, Sce

16
More details
chado-Hsa
genome-Hsa-annotation-gene
genome-Hsa-annotation-affymetrix
chado
postgresql-AffxSeq
perl-go-perl
perl-bioperl
genome-Hsa-nib
ucsc-blat
postgresql-server





17
Gene Expression Components
DAS/2 for Genotyping, GeneChip
Quant/Norm Pipeline
chado-GEC
chado-Hsa
Bioconductor
R
18
Resources

• http//www.biopackages.net
• 1000 RPMs for Fedora Core 2, 3
• Available via yum
• See site for a configuration example.

19
TODO

• Support more architectures
• Build for Cygwin OS X. RPM has been ported to
  both
• Automate package build process
• Build farm of multiple architectures,
  controllable via scheduler (GridEngine)
• Automate (if possible) inclusion of new software
  / data releases

20
TODO

• Build community interest and involvement
• Keep adding more packages!
• Keep existing packages current!

21
Acknowledgements

• Patrick Alger
• Jared Fox
• Brian OConnor
• Todd Harris
• Lincoln Stein
• Stanley Nelson

22
Anatomy of a specfile

• Metadata
• Name
• Depends
• Provides
• Changelog
• Build install script hooks
• prep
• build
• install
• post
• preun