nf-core / nf-core/genomeannotator
Fail at a run using conda profile
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- Dominant language
- Nextflow
- Stars
- 44
- Forks
- 17
- PR merge metrics
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Description
Description of the bug
I conducted a run using the following command and nextflow.config.
conda activate nf-core
nextflow run nf-core/genomeannotator -r dev -profile conda
Command error:
.command.sh: 行 2: gaas_fasta_filter_by_size.pl: not found such a command
How can I install required executables including the gaas_fasta_filter_by_size.pl script?
P.S. I tried to run with 'nextflow run nf-core/genomeannotator -r dev -profile singularity' before using -profile conda.
But I encountered the same error as "#18 Pipeline fail at REPEATMASKER_STAGELIB".
In this case, several parameter settings, including singularity.runOptions/singularity.envWhitelist in nextflow.config and SINGULARITY_BIND, had no effect.
Command used and terminal output
No response
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
Start by reproducing the command nextflow run nf-core/genomeannotator -r dev -profile conda after activating nf-core, and inspect the referenced nextflow.config. Determine why gaas_fasta_filter_by_size.pl is unavailable under the conda profile, then verify that the pipeline reaches the affected stage with the executable available. The issue provides no relevant files, terminal output, or system information.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100