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 <ashv...@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.vandenb...@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 <ashv...@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.gruen...@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*
>>>
>>> ___________________________________________________________
>>> 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/
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>>>   http://galaxyproject.org/search/mailinglists/
>>>
>>
>>
>
>
> --
> *Thanks and Regards,*
> *Ashok Varadharajan*
>
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