Re: [galaxy-dev] Python modules not found when starting with init system

2017-06-28 Thread Abbott, James
<galaxy-dev-boun...@lists.galaxyproject.org> on behalf of Gudrun Amedick <amed...@itsc.uni-luebeck.de> Sent: Wednesday, June 28, 2017 1:49:44 PM To: Maximilian Friedersdorff Cc: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Python modules not found when starting with init sy

Re: [galaxy-dev] Python modules not found when starting with init system

2017-06-28 Thread Gudrun Amedick
Hi, I know. To my understaunding of virtual environments, this shouldn't make a difference. As I said, I don't really get it. It looks like Python tries to find pysam outside of the virtual environment for some reason, that's why I'm guessing PATH. I'm curious though, and if someone knows why

Re: [galaxy-dev] Python modules not found when starting with init system

2017-06-27 Thread Gudrun Amedick
Hi, i ran into that too (on debian 8). I'm not that familiar with virtual environments but this is what I found out. It looks like the virtual environment doesn't get activated properly in the shipped ini.d-file (it is the shipped one, right?).  If I add ". /path/to/.venv/bin/activate" to it,