Small updates to handle docker IPython integration: handle tuple/lists cleanly for YAML dumping and correctly point to validation inputs for testing
Add bowtie2 to the default installation.
Restore trimming to RNA-seq pipeline.
Skip complexity calculation of pandas or statsmodels are missing.
Work on IPython docker support: enable merging of external and docker configurations on runfn, support multiprocessing runfn inside docker and handle tuple/list issues with serialization
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Create manifesst of all installed software on bcbio-nextgen installation. Query manifest for generating program version summary during runs. Expose version subcommand which dumps summarized version information to a file or stdout; this hooks into getting version information from inside a Docker container
Added support for STAR aligner based two species disambiguation
Merge branch 'master' of https://github.com/chapmanb/bcbio-nextgen
Handle logging inside of docker containers using IPython: ensure hostname setup, propogation of output for debugging. Provide test script for IPython + docker
Update import tests for conda package with new parallel structure
Provide support for Torque parameter passing with -r resources flag. Fixes #280
Merge pull request #284 from mjafin/master

Support STAR alignment disambiguation for mixed species samples. Thanks to @mjafin
Gracefully handle failures when GATK creates an empty idx file during annotation
Rework initial fastq retrieval and gunzipping to work in parallel. Explicitly move this functionality to RNA-seq and ChiP-seq pipelines and remove duplicated checks. Remove outdated demultiplexing code. Fixes #281
Enable specification of samples in multiple batches: allows a single normal sample to match with multiple tumors. Attach variant calling output to tumor samples and avoid splitting tumor/normal into separate VCFs. Fixes for filtering: avoid ploidy post-filtering and GATK filtering on MuTecT output. #285
Do not require gemini to be on PATH for data updates. Thanks to Nishanth Dandapanthu
Support infrastrcture for passing single tumor-only and tumor with normal panel inputs to cancer variant calling. Provide test case for development. #285 #273
Added support for tumor-only calling and use of normal_panel vcf in mutect.py
Merge pull request #293 from mjafin/master

Added support for tumor-only calling and use of normal_panel vcf in mute...