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<p class="MsoNormal">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:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">miso --run gff-events/indexed test-data/Galaxy29_sorted.bam --output-dir test-output/gene-psi-output --read-len 151 --paired-end 184 29<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">it errors when batching out the genes, with:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Preparing to run 4 batches of jobs...<o:p></o:p></p>
<p class="MsoNormal">Running batch of 5397 genes..<o:p></o:p></p>
<p class="MsoNormal"> - 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<o:p></o:p></p>
<p class="MsoNormal"> - Submitted thread batch-0<o:p></o:p></p>
<p class="MsoNormal">Traceback (most recent call last):<o:p></o:p></p>
<p class="MsoNormal"> File "/cm/shared/apps/python/2.7.12/lib/python2.7/site-packages/misopy/run_miso.py", line 11, in <module><o:p></o:p></p>
<p class="MsoNormal"> import misopy<o:p></o:p></p>
<p class="MsoNormal">ImportError: No module named misopy<o:p></o:p></p>
<p class="MsoNormal">Running batch of 5398 genes..<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">And errors like that for all for batches of genes. So, to make sure I actually have miso installed properly, I run the following:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Regards<o:p></o:p></p>
<p class="MsoNormal">Michael Weiner<o:p></o:p></p>
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