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B Chapman - Codefest BOSC2012

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Jan Aerts
Jan Aerts

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Codefest 2012 Brad Chapman Bioinformatics Open Source Conference, 13 July 2012
Overview 2 day coding session before BOSC 3rd year Everyone is welcome http://open-bio.org/wiki/Codefest_2012
Bio-Linux packages Galaxy packaging Moving towards intelligent configuration with available tools + wrappers during install on Bio-Linux Packaged Shrimp aligner + Trinity + additional lab software Tim Booth, Torsten Seemann, Soon Gweon https: //launchpad.net/~nebc/+archive/galaxy/+packages
BioCloudCentral Easier entry page: pulls existing clusters and pre-fills Generalize S3 buckets: 1000 genomes + loads of data Eucalyptus SQLite deployment for local installations Ntino Krampis, Enis Afgan, Dannon Baker http://biocloudcentral.org
1000 genomes documentation Work with 1000 genomes data on public resources Full workflow: BioCloudCentral, CloudBioLinux, CloudMan, Galaxy, IGV Example of complex workflow that requires full reproducibility Long http://j.mp/PRO8wp and short http://j.mp/LkZxDl versions Dawei Lin, Michael Heuer, Bertrand N´ron, Aaron Pilgrim e
CloudBioLinux packages Versions and details for all installed software Reproducibility: provide fully reproducible history of versioned software, integrated with GitHub code Accessibility: make packages available on nice web page like http://www.biogems.info/ Debian packages, Python libraries, R libraries, custom installed packages Herv´ M´nager, Brad Chapman e e

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B Chapman - Codefest BOSC2012

  • 1. Codefest 2012 Brad Chapman Bioinformatics Open Source Conference, 13 July 2012
  • 2. Overview 2 day coding session before BOSC 3rd year Everyone is welcome http://open-bio.org/wiki/Codefest_2012
  • 3. Bio-Linux packages Galaxy packaging Moving towards intelligent configuration with available tools + wrappers during install on Bio-Linux Packaged Shrimp aligner + Trinity + additional lab software Tim Booth, Torsten Seemann, Soon Gweon https: //launchpad.net/~nebc/+archive/galaxy/+packages
  • 4. BioCloudCentral Easier entry page: pulls existing clusters and pre-fills Generalize S3 buckets: 1000 genomes + loads of data Eucalyptus SQLite deployment for local installations Ntino Krampis, Enis Afgan, Dannon Baker http://biocloudcentral.org
  • 5. 1000 genomes documentation Work with 1000 genomes data on public resources Full workflow: BioCloudCentral, CloudBioLinux, CloudMan, Galaxy, IGV Example of complex workflow that requires full reproducibility Long http://j.mp/PRO8wp and short http://j.mp/LkZxDl versions Dawei Lin, Michael Heuer, Bertrand N´ron, Aaron Pilgrim e
  • 6. CloudBioLinux packages Versions and details for all installed software Reproducibility: provide fully reproducible history of versioned software, integrated with GitHub code Accessibility: make packages available on nice web page like http://www.biogems.info/ Debian packages, Python libraries, R libraries, custom installed packages Herv´ M´nager, Brad Chapman e e