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Submit a Resource
Ubuntu 8.04/Hardy with BioPerl and bioinformatics tools
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bioperl-max (v0.1.2) is a bioinformatics/BioPerl-centric machine based on Alestic/Eric Hammond's clean Ubuntu 8.04/Hardy/32-bit public install (ami-1c5db975). Many popular bioinformatics tools are here, including bwa, blast, primer3, hyphy, samtools, and others, along with R and the production packages of BioPerl.
| Submitted By: |
Mark Jensen
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| US East AMI ID: |
ami-1ad03273 |
| AMI Manifest: |
fortinbras-public/bioperl-max-0.1.2.manifest.xml |
| License: |
Public |
| Operating System: |
Linux/Unix |
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Fortinbras Research is pleased to provide this open-source bioinformatics machine to the community.
This update includes installations of short-read assembly tools maq, bwa, and samtools, and run wrappers for these applications in the updated BioPerl installations. The Perl module Bio::DB::Sam (1.07) for manipulating SAM-formatted alignments is also installed.
Trunk revisions (r16424) of the BioPerl core, bioperl-db (for creating biological databases), and bioperl-run (for wrapping and harnessing external bioinformatics tools) are installed, along with MySQL and Postgresql, R, and build-essentials. Also included in this build are perl6 (Rakudo) and parrot. Installed open-source bioinformatics apps include:
- blast
- bwa
- clustalw
- emboss
- exonerate
- hmmer
- HyPhy
- maq
- muscle
- NeXML (including Bio::Phylo)
- Phylip
- phyml
- primer3
- samtools
- t-coffee
- tigr-glimmer
More details can be found here.
We want this machine to be useful right out of the box. If something is broken or you have suggestions for improvements, please contact us. For much more info on BioPerl, visit the wiki.
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