Preparation for new release on 13.04. Update package list on 13.04. Use Anaconda as primary Python installation. General updates of package versions and improve automation. #78 #79
Revert dwgsim samtools version back to 0.1.18 to resolve compile problems
Automation fixes for anaconda and gdm
Add lightweight way to check installed versions against required in custom builds
Fix version checking with local installation. Support python installation with conda in addition to pip. Build fixes for new CloudBioLinux release
Update netcdf to new naming in EPEL. Thanks to James Cuff.
Include env.system_install PATH as part of version checking to work with installed software not on the global PATH. Thanks to James Cuff
Install vcfutils.pl as part of samtools installation
All tar file name to be specified to the _fetch_and_unpack method
Propagate tar_file_name to _get_install* methods
Provide build target for mutect and download for cosmic VCF. Supports work on MuTect in chapmanb/bcbio-nextgen#40
Re-add accidentally removed biodata.yaml config file. Fixes chapmanb/bcbio-nextgen#53
Finished fix to allow install of packages with user-specified filenames.
Merge pull request #80 from claresloggett/master

Finished fix to allow install of packages with user-specified filenames.
Do not delete galaxy's universe_wsgi.ini used during the install
Add support for installing tools in galaxy-centric way to _get_install_local method - John Chilton's indirect contribution
On the path of removing duplicate application installation methods between applications.py and bio_nextgen.py: remove cufflinks and tophat duplicate methods
Remove --noprofile to allow more reliable access to .bashrc configurations from fabric scripts across multiple bash versions and setups. Fixes chapmanb/bcbio-nextgen#56
Fix for missing -p flag in GNU mv command (use cp --parents instead)
Extract galaxy_tools into its own top-level configuration option in main.yaml, helping keep consistent modularization