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/

>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=$GALAXY_PATH/.venv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin,PYTHONHOME=$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