Yep:
PYTHONHOME=~/.venv conda --help Traceback (most recent call last): File "/home/marius/conda/bin/conda", line 3, in <module> from conda.cli import main ImportError: No module named conda.cli
On 3 March 2017 at 11:04, Ashok Varadharajan ashvark@gmail.com wrote:
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 $GALAXY_PATH/.venv --ini-paste $GALAXY_PATH/config/galaxy.ini --logdate --master --processes 3 --threads 6 --logto $GALAXY_PATH/logs/galaxy.uwsgi.log --socket 127.0.0.1:4001 --pythonpath lib --stats 127.0.0.1:9191 directory = $GALAXY_PATH umask = 022 autostart = true autorestart = true startsecs = 20 user = galaxy environment = PATH=$GALAXY_PATH/.venv/bin:/u sr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin, *PYTHONHOME=$GALAXY_PATH/.venv*,DRMAA_LIBRARY_PATH=/usr/local/l ib/libdrmaa.so numprocs = 1 stoplight = INT startretries = 15 process_name = web%(process_num)s
[program:handler] command = $GALAXY_PATH/.venv/bin/python ./lib/galaxy/main.py -c $GALAXY_PATH/config/galaxy.ini --server-name=handler%(process_num)s --log-file=$GALAXY_PATH/logs/
galaxy_handler%(process_num)s.log
directory = $GALAXY_PATH process_name = handler%(process_num)s numprocs = 3 umask = 022 autostart = true autorestart = true startsecs = 20 user = galaxy environment = PATH=$GALAXY_PATH/.venv/bin:/u sr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin, *PYTHONHOME=$GALAXY_PATH/.venv*,DRMAA_LIBRARY_PATH=/usr/local/l ib/libdrmaa.so startretries = 15
Thanks Ashok
On Fri, Mar 3, 2017 at 10:37 AM, Marius van den Beek < m.vandenbeek@gmail.com> wrote:
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 /bioinfo/guests/mvandenb/galaxy/.venv --ini-paste /bioinfo/guests/mvandenb/gx/config/galaxy.ini --logdate --master --processes 2 --threads 2 --logto /home/galaxy/galaxy/uwsgi.log --socket 127.0.0.1:4001 --pythonpath lib --stats 127.0.0.1:9191 directory = /bioinfo/guests/mvandenb/galaxy umask = 022 autostart = true autorestart = true startsecs = 20 user = galaxy environment = /bioinfo/guests/mvandenb/galaxy/.venv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin numprocs = 1 stopsignal = INT startretries = 15
Best, Marius
On 3 March 2017 at 10:29, Ashok Varadharajan ashvark@gmail.com wrote:
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 issue when installing tools from the toolshed.
I also tried updating the conda using "conda update conda" but didnt help.
Do i have to adjust the PYTHONPATH in my supervisor configuration ?
Regards, Ashok
On Thu, Mar 2, 2017 at 10:14 PM, Björn Grüning < bjoern.gruening@gmail.com> wrote:
Hi Ashok,
this seems to be a problem with your conda installation.
See for example here: https://github.com/conda/conda/issues/2463 Can you update your conda manually?
Cheers, Bjoern
Am 02.03.2017 um 17:47 schrieb Ashok Varadharajan:
ImportError: No module named conda.cli.main
-- *Thanks and Regards,* *Ashok Varadharajan*
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-- *Thanks and Regards,* *Ashok Varadharajan*