galaxyproject / galaxyproject/tools-devteam
vcftools dependencies: tabix and bgzip
- 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
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