Allow creation of tool specific temporary directories, avoiding deletion when using CloudBioLinux inside of CloudBioLinux. Fixes #120
Avoid checking for freec installation if not a supported platform. Fixes chapmanb/bcbio-nextgen#124
Update grabix with speed fixes for indexing and add pbgzip build: parallel block gzip
Don't set galaxy uid explicitly but use the next available one (accompanied with changes to the config for proftpd)
Bump freebayes to latest version. Resolves issues with NA12878 test calling
Merge branch 'master' of https://github.com/chapmanb/cloudbiolinux
Build target for biobambam, providing bamtofastq
Add biobambam to minimal ngs tool flavor. Avoid versioncheck errors when no version found on commandline
Provide hook to avoid updating ~/.bashrc with PATH and LD_LIBRARY_PATH for local installs
Merge branch 'master' of github.com:chapmanb/cloudbiolinux
Add libtool and pkg-config dependencies for biobambam autoconf. Fixes #121
Move to release versions of biobambam that do not require autoconf. gt1/biobambam#4