Mega patch of fixes to get installation working cleanly on localhost CentOS builds: add localhost builds for additional cloudman tools. Removes problem perl, python and ruby builds. Updates to use anaconda throughout and clean up pip temp directories. Lots of bug fixes. Thanks to @andersje. Fixes #87. Fixes #89. Fixes #90. Fixes #91
Proteomics: Fix small syntax error in Galaxy-P's tools.yaml file.
Proteomics: More updates to to Galaxy-P's tools.yaml file. This contains some backward compat stuff that should eventually be eliminated.
Fix typo
Ensure python installations use sudo for global installs and standard user for anaconda installs. Fixes issues on CentOS with root bin. Thanks to @andersje
Merge branch 'master' of github.com:chapmanb/cloudbiolinux
Ensure leiningen build works on localhost installations. #93
Provide download target for latest GATK protected that requires manual download step. Include as part of bcbio-nextgen builds. chapmanb/bcbio-nextgen#83, chapmanb/bcbio-nextgen#84
Correctly assign additional custom flavor packages to groups for running
Allow conditional inclusion/exclusion of Galaxy tools and/or tool 'provides' synonyms based on fabric environment variables. Add 'if: <variable>' to the yaml config below the tool or the provides will cause the tool configuration to only be installed if that fabric variable is True (according to the _read_boolean function - i.e. if the variable is "true", True, 'YES', etc...). Likewise if an 'unless: <variable>' appears the tool will be installed unless the fabric variable is True.
Correctly ignore additional custom packages when not specified. Thanks to @roryk
Retrieve VCF index files as part of download to avoid needing to create them. chapmanb/bcbio-nextgen#85
Added the STAR spliced read aligner.
Added RNA-SeQC from the Broad.
Typo fixed.
Merge pull request #96 from roryk/master

Added the STAR spliced read aligner.
Add STAR and rnaseqc to default packages for CloudBioLinux and minimal bcbio-nextgen install
Ubuntu 13.04 work: update STAR aligner to latest alpha release that compiles. Fixes #98. Do not re-install distribute on anaconda systems to avoid bx-python install error. Fixes #97
Update vcftools to the latest version
Added gtfToGenePred to ucsc_tools.