Merge pull request #159 from glebkuznetsov/master

Don't reconfigure fabric env in fabfile.install_brew() if automated install.
For remote env.safe_run_output disable shell by default
Not needed because of fixed env.safe_run_output
Merge pull request #160 from nuada/ls-color-fix

Fixed disabling of ls color output
Include Staden io_lib with support for CRAM indexing and retrieval by position
Attempt to work around hang when checking for leiningen during reprocessing
Add cramtools and rtg-tools support through brew installs. Remove old custom cramtools install
Fix for karyotype sorting multifasta genomes.

Some of the UCSC style genomes are in multifasta format, which
was not being split into individual chromosomes before
being karyotype sorted. This fixes that issue.
Skip creating the STAR index if the GTF file is not found.
Generalize dbSNP preparation script.
Update featureCounts to 64 bit version. Support OSX installs.
Merge branch 'master' of github.com:chapmanb/cloudbiolinux
Fix for string formatting issue.
Provide downloads for annotated repeat regions for human SNP indel and structural variant calling: low complexity regions from Heng Li and telomeres/centromeres from delly
Fix for homebrew causing a failedOSX installation.

This checks for homebrew first before trying to install it
again. Fixes #155. Partial progres on chapmanb/bcbio-nextgen#396.
Fix Tophat installation on OSX.
Add directory to search for find(1).

OSX find(1) needs this set explicitly:

rory@clotho:~$ find -name "foo"
find: illegal option -- n
Remove pbgzip which fails to compile on Mac and is not currently used. Add samblaster and speedseq builds for lumpy SV calls
Remove use of -r sed flag for snpEff; fix for MacOSX. Remove unused builds that have been moved over to homebrew
Add camFam3 dbSNP resource to automatic downloads. Swap mm10 to use bgzipped and tabix indexed files