search

galaxyproject / tools-devteam

Contains a set of Galaxy Tools mostly written by the Galaxy Team.
36 stars 92 forks source link

vcftools dependencies: tabix and bgzip #111

Open lparsons opened 9 years ago

lparsons commented 9 years ago

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 commented 9 years ago

@lparsons this is an oversight! Thanks for reporting!

nsoranzo commented 9 years ago

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 https://github.com/galaxyproject/tools-iuc/issues/146 .

aguynamedben commented 8 years ago

+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.