Re: [galaxy-dev] Problem with installing tools using Conda

Yep: PYTHONHOME=~/.venv conda --help Traceback (most recent call last): File "/home/marius/conda/bin/conda", line 3, in from conda.cli import main ImportError: No module named conda.cli ​ On 3 March 2017 at 11:04, Ashok Varadharajan wrote: > Hi Marius, > > Thanks for

Re: [galaxy-dev] Problem with installing tools using Conda

Hi Marius, Thanks for your reply. Below is my supervisor configuration and it looks similar to yours except "PYTHONHOME" in the environment section. Do you think that would be the issue ? [supervisord] [program:galaxy_web] command = $GALAXY_PATH/.venv/bin/uwsgi --virtualenv

Re: [galaxy-dev] Problem with installing tools using Conda

Hi Ashok, You should not set the PYTHONPATH in supervisor. That is indeed going to conflict with conda. If you are using uwsgi you can use something like this: [program:galaxy_web] command = /bioinfo/guests/mvandenb/galaxy/.venv/bin/uwsgi --virtualenv

Re: [galaxy-dev] Problem with installing tools using Conda

Thanks John and Bjoern for your reply. Conda is working properly when i trigger it manually as a galaxy user. (example: $conda_prefix/conda install bwa -c bioconda) I tried to remove the conda_prefix directory and it was reinstalled after restarting the galaxy. But still I am getting the same

Re: [galaxy-dev] Problem with installing tools using Conda

I've never seen anything like this before - I am sorry. Hopefully someone else will have a more concrete idea. Does that Conda executable work on the command line? I'd try removing the whole Conda folder and rebuilding it. Is it possible the install was corrupted at some point - maybe during