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:
command = /bioinfo/guests/mvandenb/galaxy/.venv/bin/uwsgi
--virtualenv /bioinfo/guests/mvandenb/galaxy/.venv --ini-paste
--master --processes 2 --threads 2 --logto
/home/galaxy/galaxy/uwsgi.log --socket 127.0.0.1:4001 --pythonpath lib
directory = /bioinfo/guests/mvandenb/galaxy
umask = 022
autostart = true
autorestart = true
startsecs = 20
user = galaxy
numprocs = 1
stopsignal = INT
startretries = 15
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 ?
> On Thu, Mar 2, 2017 at 10:14 PM, Björn Grüning <bjoern.gruen...@gmail.com>
>> 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?
>> 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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