How to import argparse when I am using qsub in Linux server?
Question: I want to use CoNIFER, which is a python program for bioinformatics.

So, I wrote a script for qsub because of my institute's rule.

Here is my qsub script. I inserted enter in front of -- to show it clear.

    
    
    #!/bin/bash
    #$ -N oh
    #$ -cwd
    cd /usr/etc/GRAPE_ENV/Python/
    python /home/osj118/tools/conifer_v0.2.2/conifer.py rpkm
    --probes/home/osj118/input/GBM/Gastric/Exome_probe/Exome_probe_capture_library_coordinate.txt
    --input /scratch/Gastric_cell_bam/AGS_2.fastq.gz_Illumina_exome_Exome.RGadded.marked.realigned.fixed.recal.bam
    --output /home/osj118/output/AGS_rpkm.txt
    cd /home/osj118/pyscripts
    

CoNIFER did not work and show error message that

> ImportError: No module named argparse

I already used `sys.append.path` function but it failed to solve my problem.

Strangely, when I ran batch job, CoNIFER worked correctly without any error
message.

As batch job violates the rule, I want to use qsub to work in Linux server.

Please give me any solution for this situation.


Answer: This smells like a pythonpath problem. The pythonpath determines where python
can find the required modules. If you installed CoNIFER in a directory
together with the packages it uses, then Python will find the packages only if
they are on the pythonpath.

You can specify the pythonpath as follows:

export PYTHONPATH=/directory where CoNIFER is installed

