galaxy_handler%(process_num)s.log
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:/ usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin, *PYTHONHOME=$GALAXY_PATH/.venv*,DRMAA_LIBRARY_PATH=/usr/local/ lib/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/ 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:/ usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin, *PYTHONHOME=$GALAXY_PATH/.venv*,DRMAA_LIBRARY_PATH=/usr/local/ lib/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*