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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