Hi,

During the installation or galaxy instance, I set up a directory to install all the python dependencies. Basically, whenever I install python modules, I do something like:

python setup.py install --prefix=/my/python/dir

as a result, there are tons of stuff installed there. I added this path to PYTHONPATH.

The reason I do this is that I don't want to use sudo to install galaxy python modules.

Now the problem...I was hoping not to use virtual env. However galaxy is set to use it's own venv, and during the course of starting, it will unset the PYTHONPATH. That caused that installed tools didn't work because it could not find the modules installed.

Here is one example of how it is not working. The tool generated the following command in the script:

gca -b /media/libraryfiles/galaxy-data-store/database/files/000/dataset_44.dat --span=3000 -g /media/libraryfiles/dep/cistrome-static-lib/ceaslib/GeneTable/mm9 --name=gca_out >& /media/libraryfiles/galaxy-data-store/database/files/000/dataset_95.dat

cp gca_out.xls /media/libraryfiles/galaxy-data-store/database/files/000/dataset_94.dat

I could run that command in the terminal successfully, but not in the galaxy. It keeps reporting error that gca_out.xls isn't there. With the PYTHONPATH unset, when I run that command, I would get:

Traceback (most recent call last):

File "/media/libraryfiles/dep/python/bin/gca", line 32, in <module>

import CEAS.inout as inout

ImportError: No module named CEAS.inout

Once I put the PYTHONPATH back,

export PYTHONPATH=/media/libraryfiles/dep/python/lib/python2.7/site-packages

then that gca command would generate the correct output file.

I tried to use

sh run.sh --skip-venv

However, it keeps giving me errors. It seems those were from not able to install the dependencies listed in requirements.txt.

I then installed those dependencies to my python directory as well. During the course had to remove some that came with system, and install the newer ones.

Now it seems to be working. I'm just wondering, is this a good way to using system python with all the dependencies I installed?

Thanks,

Rui