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cerebis / qc3C

Reference-free quality assessment for Hi-C sequencing data
GNU Affero General Public License v3.0
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samtools missing from qc3C docker container path #45

Closed koadman closed 3 years ago

koadman commented 3 years ago

while attempting to run qc3c in bam mode via docker:

docker run -v `pwd`:/app cerebis/qc3c bam --library-kit phase --fasta assembly.fasta.gz --bam reads2ref.bam --output-path outputbam
INFO     | 2021-03-18 00:49:22,881 |    main | Library kit phase declares enzymes ['Sau3AI', 'MluCI']
INFO     | 2021-03-18 00:49:22,881 | qc3C.ligation | No cut-site database cache found for digest involving MluCI, Sau3AI
INFO     | 2021-03-18 00:49:22,887 | qc3C.ligation | Building cut-site database against reference sequence and MluCI, Sau3AI
100%|██████████| 3169/3169 [00:20<00:00, 156.83it/s]
INFO     | 2021-03-18 00:49:44,343 | qc3C.ligation | Saving cut-site database for reuse
INFO     | 2021-03-18 00:49:45,346 | qc3C.bam_based | Accepting all usable reads
INFO     | 2021-03-18 00:49:45,346 | qc3C.utils | Random seed was not set, using 28808787
INFO     | 2021-03-18 00:49:45,346 | qc3C.bam_based | Beginning analysis...
INFO     | 2021-03-18 00:49:45,346 | qc3C.bam_based | Counting alignments in reads2ref.bam
ERROR    | 2021-03-18 00:49:45,346 |    main | AssertionError('required tool samtools was not found on path')
cerebis commented 3 years ago

Samtools is now defined as a dependency in the qc3C conda package.