umi_tools dedup fails with old pysam

Hello! After updating umi_tools from 1.0.1 to 1.1.0 the dedup program fails with an error:

sort: unrecognized option '--no-PG'
Traceback (most recent call last):
  File "/cludisk/Projects/Testing/Chromatest/workflow/.snakemake/conda/4046b958/bin/umi_tools", line 11, in <module>
    sys.exit(main())
  File "/cludisk/Projects/Testing/Chromatest/workflow/.snakemake/conda/4046b958/lib/python3.6/site-packages/umi_tools/umi_tools.py", line 61, in main
    module.main(sys.argv)
  File "/cludisk/Projects/Testing/Chromatest/workflow/.snakemake/conda/4046b958/lib/python3.6/site-packages/umi_tools/dedup.py", line 373, in main
    pysam.sort("-o", sorted_out_name, "-O", sort_format, "--no-PG", out_name)
  File "/cludisk/Projects/Testing/Chromatest/workflow/.snakemake/conda/4046b958/lib/python3.6/site-packages/pysam/utils.py", line 75, in __call__
    stderr))
pysam.utils.SamtoolsError: 'samtools returned with error 1: stdout=, stderr=Usage: samtools sort [options...] [in.bam]\nOptions:\n  -l INT     Set compression level, from 0 (uncompressed) to 9 (best)\n  -m INT     Set maximum memory per thread; suffix K/M/G recognized [768M]\n  -n         Sort by read name\n  -t TAG     Sort by value of TAG. Uses position as secondary index (or read name if -n is set)\n  -o FILE    Write final output to FILE rather than standard output\n  -T PREFIX  Write temporary files to PREFIX.nnnn.bam\n      --input-fmt-option OPT[=VAL]\n               Specify a single input file format option in the form\n               of OPTION or OPTION=VALUE\n  -O, --output-fmt FORMAT[,OPT[=VAL]]...\n               Specify output format (SAM, BAM, CRAM)\n      --output-fmt-option OPT[=VAL]\n               Specify a single output file format option in the form\n               of OPTION or OPTION=VALUE\n      --reference FILE\n               Reference sequence FASTA FILE [null]\n  -@, --threads INT\n               Number of additional threads to use [0]\n'

Updating pysam from 0.15.3 to 0.16.0.1 fixes this error. Please correct requirements.txt.

[karl616]

That is correct. I’ll add the dependencies explicitly in my environment. That will work for now

FYI; BioConda being a community project, it is very easy to provide a PR. And after being accepted as a contributor, you can even control the addition… They seem to have taken that further since I was active: https://bioconda.github.io/contributor/updating.html

[IanSudbery]

Okay, I’m wrong(ish). The bioconda team are going to move the broken build (build 0) to the their “broken” channel, which means it shouldn’t be available for normal installations. This change has been made and will take about an hour to percolate through the CDN.

BTW mamba gets the right build of umi_tools and pysam right off the bat.