[miso-users] Problems with script on HPC

[Weiner, Michael]

I recently installed miso on our HPC under python 2.7.12 using pip and it generally seems to work. I am however running into an issue. So for our users to use miso, they must load the module (module load python/2.7.12) and then they are able to call miso. When (for testing) I try to run:

miso --run gff-events/indexed test-data/Galaxy29_sorted.bam --output-dir test-output/gene-psi-output --read-len 151 --paired-end 184 29

it errors when batching out the genes, with:

Preparing to run 4 batches of jobs...
Running batch of 5397 genes..
  - Executing: python /cm/shared/apps/python/2.7.12/lib/python2.7/site-packages/misopy/run_miso.py --compute-genes-from-file "/home/mweiner/darnmiso/test-output/gene-psi-output/batch-genes/batch-0_genes.txt" /home/mweiner/darnmiso/test-data/Galaxy29_sorted.bam /home/mweiner/darnmiso/test-output/gene-psi-output --read-len 151  --paired-end 184.0 29.0 --settings-filename /cm/shared/apps/python/2.7.12/lib/python2.7/site-packages/misopy/settings/miso_settings.txt
  - Submitted thread batch-0
Traceback (most recent call last):
  File "/cm/shared/apps/python/2.7.12/lib/python2.7/site-packages/misopy/run_miso.py", line 11, in <module>
    import misopy
ImportError: No module named misopy
Running batch of 5398 genes..

And errors like that for all for batches of genes. So, to make sure I actually have miso installed properly, I run the following:

python2.7 /cm/shared/apps/python/2.7.12/lib/python2.7/site-packages/misopy/run_miso.py --compute-genes-from-file "/home/mweiner/darnmiso/test-output/gene-psi-output/batch-genes/batch-0_genes.txt" /home/mweiner/darnmiso/test-data/Galaxy29_sorted.bam /home/mweiner/darnmiso/test-output/gene-psi-output --read-len 151  --paired-end 184.0 29.0 --settings-filename /cm/shared/apps/python/2.7.12/lib/python2.7/site-packages/misopy/settings/miso_settings.txt

which runs correctly and completes. So my question is, why am I getting the missing module error above when I don't get it running the individual gene batches.

Regards
Michael Weiner

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