Comments (1)
Actually, more broadly should check to see whether the dependencies are installed. Not guaranteed they'll come in with conda if users install via pip
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Related Issues (20)
- Make --no_SRR_parsing default
- Figure out why iMicrobe breaks on circleCI
- fasterq-dump error: HOT 3
- Add callout to FAQ in main README
- Version 0.5.0 breaks numpy HOT 3
- SRA metadata not including BioSample attributes HOT 4
- Refactor code
- Use "conda deactivate" instead of "source deactivate"
- pigz attempting to zip files that don't exist HOT 1
- Dependency check
- Not compatible with Python 3.7? HOT 4
- Allow users to pass custom args to fast(er)q-dump
- grabseqs and geofetch
- error handling when sra accession doesn't exist / doesn't return runs HOT 1
- Add support to download data from EBI HOT 3
- Add support to download data from National Genomics Data Center
- All grabseqs SRA downloads failing HOT 10
- Grabseqs error HOT 9
- grabseqs sra -l PRJDB5400 pigz not found, using gzip Traceback (most recent call last): File "/home/tools/anaconda3/bin/grabseqs", line 8, in <module> sys.exit(main()) File "/home/tools/anaconda3/lib/python3.8/site-packages/grabseqslib/__init__.py", line 58, in main metadata_agg = process_sra(args, zip_func) File "/home/tools/anaconda3/lib/python3.8/site-packages/grabseqslib/sra.py", line 27, in process_sra acclist, metadata_agg = get_sra_acc_metadata(sra_identifier, File "/home/tools/anaconda3/lib/python3.8/site-packages/grabseqslib/sra.py", line 97, in get_sra_acc_metadata run_col = lines[0].index("Run") ValueError: 'Run' is not in list HOT 1
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