chapmanb/cloudbiolinux

Remove custom GEMINI build, replaced by conda. Fixes #211

Update cufflinks to point to new binary locations. Use homebrew binar… …

…y recipe instead of custom build. Thanks to Severine Catreux

Remove plink_seq custom tool which has a dead download page. Fixes #182

Update varscan to latest version. Remove duplicate custom snpEff whic… …

…h is no longer needed with bcbio upgrades. Install snap development version by default

Remove GATK lite installation due to broken ftp and version getting d… …

…ated. Fixes chapmanb/bcbio-nextgen-vm#9

Update to latest version of snpEff, GEMINI and VEP. Prefer brew insta… …

…lls for snpEff and VEP, maintaining old snpEff for short-term back-compatibility

Remove pbgzip which fails to compile on Mac and is not currently used… …

…. Add samblaster and speedseq builds for lumpy SV calls

Add cramtools and rtg-tools support through brew installs. Remove old… …

… custom cramtools install

Avoid standard seal/pydoop installation. Requires new dependencies an… …

…d best suited for a custom flavor devoted to Cloud/Hadoop

Move biobambam and libmaus build to brew packages instead of custom b… …

…uilds. Clean up unused custom builds

Merge branch 'master' of github.com:chapmanb/cloudbiolinux

Merge pull request #154 from JCVI-Cloud/master …

updates to vcr.py

Move to homebrew package for RNA-seq STAR aligner

Add featureCounts. …

This will replace htseq-count; it has similar functionality and
is about 10x faster.

Move FreeBayes build to use brew recipe. Add Platypus caller

Add AlienTrimmer to the bio_nextgen custom installer.

Update to latest variant effects predictor with batch download. Only … …

…install API files and not cache files. Fixes #138. Fixes #116

Add homebrew versions of vcflib and glia packages, and make available… …

… to bcbio-nextgen installer. chapmanb/bcbio-nextgen#204

Merge branch 'master' of github.com:chapmanb/cloudbiolinux

Add fastx_toolkit as homebrew dependency instead of custom build. Inc… …

…lude in bcbio-nextgen installation

Use cloudman meta installation target instead of proftpd and sge spec… …

…ific ones. Meta target installs users and configures cloudman first. Fixes #136

Added disambiguate to bionextgen.

Remove custom GNU parallel custom target, replacing with brew GNU par… …

…allel build. Fixes chapmanb/bcbio-nextgen#160

Re-enable additional brew-based builds with --env=inherit set thanks … …

…to latest linuxbrew that allows use of external compiler environment Linuxbrew/legacy-linuxbrew#29

Update sambamba to latest version with multicore support. Move to a h… …

…omebrew recipe and remove older custom script.

Remove homebrew build targets requiring more complicated builds until… …

… we get a better handle on directing the gcc to use

Bump biobambam version and avoid custom novosort included with brew n… …

…ovoalign

Enable homebrew/linuxbrew integration as part of default CloudBioLinu… …

…x installation. Replace custom packages with homebrew equivalents. Update ngs_pipeline_minimal flavor for bcbio-nextgen builds

Use new shared wget functionality to retrieve code and data files, av… …

…oiding potential issues with partial downloads and cleanly handling all wget peculiarities. Fixes chapmanb/bcbio-nextgen#127

Build target for biobambam, providing bamtofastq

Update grabix with speed fixes for indexing and add pbgzip build: par… …

…allel block gzip

Merge branch 'master' of git://github.com/chapmanb/cloudbiolinux

Update GATK protected build to latest 2.7 version

Add support for MacOX Homebrew (and Linuxbrew port) package manager. … …

…Provide preliminary framework for supporting MacOSX but needs testing and additional work

Added Control-FREEC to bio_nextgen. …

This is a CNV caller: http://bioinfo-out.curie.fr/projects/freec/