Biopackages.net

Operating System Packages for BioinformaticsAllen Day2005.05.17

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

GMOD target audience Small MODs

Package Dependency Graph

Dependencies What the package provides

chado

chado-Hsa

genome-Hsa-nib ucsc-blat

genome-Hsa-annotation-affymetrix

genome-Hsa-annotation-gene

postgresql-AffxSeq

postgresql-server

perl-bioperl

obo-core

perl-go-perl

Dependencies

Build Dependency Installation Dependency

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)

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.

What’s available?

RPM packages only right now Primary focus on Fedora Core 2

Some RPMs also available for Fedora Core 3 RedHat 9 Cygwin

What’s available?

Three primary foci Applications Libraries Data sets

Applications

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

What’s available?

Libraries Bioperl R & Bioconductor Squid EMBOSS

What’s available?

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

structure

What’s 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)

GMOD Components Available

chado-Hsa gbrowse textpresso

gmod-web-Hsa

turnkey

chado

das2-Hsa

apollo-Hsa

cmap-Hsa

‘Hsa’ can be substituted for your organismCurrently built for ‘Cel’, ‘Hsa’, ‘Sce’

ucsc-BLATgenome-Hsa-nib

More details…

chado

chado-Hsa

genome-Hsa-nib ucsc-blat

perl-go-perl

genome-Hsa-annotation-affymetrix

genome-Hsa-annotation-gene

postgresql-AffxSeq

postgresql-serverperl-bioperl

…… ………

Gene Expression Components

chado-Hsa BioconductorR

Quant/NormPipeline

chado-GEC

DAS/2 forGenotyping,GeneChip

Resources

http://www.biopackages.net ~1000 RPMs for Fedora Core 2, 3 Available via yum

See site for a configuration example.

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

TODO

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

Acknowledgements

Patrick Alger Jared Fox Brian O’Connor Todd Harris Lincoln Stein Stanley Nelson