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

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
--span=3000 -g
--name=gca_out >&
    cp gca_out.xls

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

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?

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