chapmanb/bcbio-nextgen — pull request #109 by lbeltrame (2013-09-13 14:51:10+00:00)
Title: Initial support for Somatic Sniper

This pull request fixes #66 and is related also to #67. Like almost all callers I contributed earlier, this version will likely not work and needs some input and review.
I'm mostly interested in how to look for the Somatic Sniper binary, given that:

* it is called "bam-somaticsniper" instead of plain "somaticsniper"
* It should be looked in PATH first (like bwa and other aligners)

Where should I look for inspiration?
Also I still need to see what files does Somatic Sniper produces when input does not contain variants or no somatic variants (to see if I have to hook `write_empty_vcf` manually).

Aside that (this is mainly for CloubBioLinux deployment, should this get merged), is the fact that no released version of Somatic Sniper supports tumor and normal sample names, but there is in git, so for now it's not possible to really add a check for version (see the FIXME).