doesn't pickup qcmodule which is on the path

[MNoon]

I have installed RSeQC on HPC into my access directory (no root). I have setup the paths to the "site-packages" where  qcmodule resides. See below

/unsupported/nirav/RSeQC/2.6.4/cm/shared/uaapps/python/2.7.11/lib/python2.7/sitepackages/:/unsupported/nirav/RSeQC/2.6.4/cm/shared/uaapps/python/2.7.11/bin/:/cm/shared/uaapps/python/2.7.11/bin:/cm/shared/uaapps/R/3.4.1/bin:/home/u8/mnoon/modules/perl5/bin:/cm/local/apps/gcc/6.1.0/bin:/cm/shared/apps/pbspro/current/sbin:/cm/shared/apps/pbspro/current/bin:/cm/shared/uabin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/sbin:/usr/sbin:/cm/local/apps/environment-modules/3.2.10/bin:/home/u8/mnoon/cyverse-cli/bin:/home/u8/mnoon/bin:

but it still complains about missing qc module:

bam2fq.py --version

Traceback (most recent call last):

  File "/unsupported/nirav/RSeQC/2.6.4/cm/shared/uaapps/python/2.7.11/bin/bam2fq.py", line 23, in <module>

    from qcmodule import SAM

ImportError: No module named qcmodule

OR

bam2wig.py --version

Traceback (most recent call last):

  File "/unsupported/nirav/RSeQC/2.6.4/cm/shared/uaapps/python/2.7.11/bin/bam2wig.py", line 20, in <module>

    from bx.bitset import *

ImportError: No module named bx.bitset

How can this be fixed?

Thanks,

M

[Liguo Wang]

Hi,

you need to setup  PYTHONPATH not PATH, for example:

export  PYTHONPATH==/unsupported/nirav/RSeQC/2.6.4/cm/shared/uaapps/python/2.7.11/lib/python2.7/sitepackages/

should be in your .bash_profile

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