ImportError: No module named conda.cli.main

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(a)gmail.com&gt; 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* ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

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(a)gmail.com&gt; 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(a)gmail.com&gt; 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(a)gmail.com&gt; 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* >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > > -- *Thanks and Regards,* *Ashok Varadharajan*