vcftools dependencies: tabix and bgzip

[lparsons]

It seems like the tools in the vcftools collection require both bgzip and tabix (see e.g. https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/vcftools/vcftools_subset/vcftools_subset.xml). However, they are not installed as a dependency from the ToolShed. Are these tools that should be installed on the galaxy user's path, or is this simply a dependency oversight?

[bgruening]

@lparsons this is an oversight! Thanks for reporting!

[nsoranzo]

bgzip and tabix are now included in HTSlib, so a dependency on (still-to-be-updated) samtools 1.2 would probably be more future-proof. See galaxyproject/tools-iuc#146 .

[aguynamedben]

+1 I ran into this following the CloudMan instructions. I failed to download my SSH key on cluster launch, now I have to restart my cluster in order to get a new key just so I can install bgzip.