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(a)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(a)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(a)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*