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  • DEXseq in a docker environment

    I am attempting to run a DEXseq python script to count reads from a STAR alignment to the human genome. I am trying to a “docker” procedure to setup the environment and execute the program.

    docker pull quay.io/biocontainers/bioconductor-dexseq:1.24.0--py36r3.4.1_1


    Here is the docker result:

    docker run -it -v ~/Meissner-Tsao-April2018:/data musc/dexseq dexseq_count.py data/Homo_sapiens.GRCh38.92_DEXSeq.gff data/STAR_aligned_5021_S20_L005Aligned.sortedByCoord.out.bam data/STAR_aligned_5021_S20_L005_STAR_dexseq_count_fpsr.txt -f bam -p yes -s no -r pos
    Traceback (most recent call last):
    File "/usr/local/bin/dexseq_count.py", line 98, in <module>
    features[f.iv] += f
    File "python3/src/HTSeq/_HTSeq.pyx", line 451, in HTSeq._HTSeq.ChromVector.__iadd__
    File "python3/src/HTSeq/_HTSeq.pyx", line 466, in HTSeq._HTSeq.ChromVector.apply
    File "python3/src/HTSeq/_HTSeq.pyx", line 449, in HTSeq._HTSeq.ChromVector.__iadd__.addval
    TypeError: unhashable type: 'GenomicFeature'


    The GFF was prepared ash show here

    docker run -it -v ~/Meissner-Tsao-April2018:/data musc/dexseq dexseq_prepare_annotation.py data/Homo_sapiens.GRCh38.92.gtf data/Homo_sapiens.GRCh38.92_DEXSeq.gff




    appears to discuss the same issue I have but refers to no solution.

    The python version in the docker is
    docker run -it -v ~/Meissner-Tsao-April2018:/data musc/dexseq python -V
    Python 3.6.4

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