galaxyproject / galaxyproject/tools-devteam

vcftools dependencies: tabix and bgzip

Open
#111 3 comments 0 reactions 0 assignees View on GitHub
bug
Dominant language
Python
Stars
37
Forks
94
PR merge metrics
No merged PRs in 30d

Description

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?

Contributor guide

Open the contributing guide

Research direction

Start by reviewing tool_collections/vcftools/vcftools_subset/vcftools_subset.xml and the ToolShed dependency conventions for vcftools. Confirm whether tabix and bgzip must be declared as dependencies or supplied on the Galaxy user's PATH; done means the installation requirement is resolved or clearly documented.

Written by the indexing model from the issue text.

Assessment

Domain
bioinformatics, tooling
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
30/100

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