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Old 04-23-2018, 01:39 PM   #1
Starr_Hazard
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Location: South Carolina

Join Date: Nov 2010
Posts: 19
Default 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


https://support.bioconductor.org/p/106685/

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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