Add NCBI hg38 and hg19 BSgenomes to the containers
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bug
- Dominant language
- Nextflow
- Stars
- 14
- Forks
- 9
- PR merge metrics
- No merged PRs in 30d
Description
Description of the bug
Currently the containers used for all Fraser and SpliceCounts modules don't include NCBI hg38 and hg19 support. This should be added since the pipeline does support those references. This currently causes the following error:
Error in .stopOnAvailablePkg(genome) :
BSgenome.Hsapiens.NCBI.GRCh38 package is not currently installed.
You first need to install it, which you can do with:
library(BiocManager)
install("BSgenome.Hsapiens.NCBI.GRCh38")
Calls: getBSgenome ... .getInstalledPkgnameFromGenome -> .stopOnAvailablePkg
Execution halted
Command used and terminal output
Relevant files
No response
System information
No response
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Locate the container definitions used by the Fraser and SpliceCounts modules, then review how installed R/Bioconductor packages are specified. Confirm that the NCBI hg38 and hg19 BSgenome packages are available in both containers and verify the pipeline can use those references without the reported missing-package error.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 58/100