I've never seen anything like this before - I am sorry. Hopefully
someone else will have a more concrete idea.

Does that Conda executable work on the command line?

I'd try removing the whole Conda folder and rebuilding it. Is it
possible the install was corrupted at some point - maybe during
install?

The just released Galaxy 17.01 has much better logging of Conda
problems and a script that can be used outside of Galaxy to explicitly
setup Conda.

-John

On Thu, Mar 2, 2017 at 11:47 AM, Ashok Varadharajan <ashv...@gmail.com> wrote:
> Dear Team,
>
> I have problem with the installation of tools using conda. I am getting
> following error message when i try to install tools from galaxy. I tried to
> install these tools manually with the same conda used by the galaxy and it
> worked. Can anyone help us to solve this issue ?
>
> Traceback (most recent call last):
>   File "/xxxx/xxxxx/xxxx-xxxx/conda//bin/conda", line 4, in <module>
>     from conda.cli.main import main
> ImportError: No module named conda.cli.main
> galaxy.tools.deps.resolvers.conda DEBUG 2017-03-02 17:35:49,759 Removing
> failed conda install of samtools, version '1.3.1'
> Traceback (most recent call last):
>   File "/xxxx/xxxxx/xxxx-xxxx/conda//bin/conda", line 4, in <module>
>     from conda.cli.main import main
> ImportError: No module named conda.cli.main
> galaxy.tools.deps.resolvers.conda DEBUG 2017-03-02 17:35:49,941 Removing
> failed conda install of samtools, version 'None'
> Traceback (most recent call last):
>   File "/xxxx/xxxxx/xxxx-xxxx/conda//bin/conda", line 4, in <module>
>     from conda.cli.main import main
> ImportError: No module named conda.cli.main
> galaxy.tools.deps.resolvers.conda DEBUG 2017-03-02 17:35:50,142 Removing
> failed conda install of bwa, version '0.7.15'
> Traceback (most recent call last):
>   File "/xxxx/xxxxx/xxxx-xxxx/conda//bin/conda", line 4, in <module>
>     from conda.cli.main import main
> ImportError: No module named conda.cli.main
>
> We are running galaxy-16.07 behind the proxy using nginx, uwsgi and
> supervisor in scientific linux 7. Below are the details of galaxy.ini and
> supervisor configuration.
>
>
> ### galaxy.ini
>
> conda_prefix = /xxxx/xxxxx/xxxx-xxxx/conda/
> #conda_exec =
> conda_debug = False
> conda_ensure_channels = r,bioconda,iuc
> #conda_auto_install = False
> #conda_verbose_install_check=False
> conda_auto_init = True
>
> ### supervisor
>
> [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 and Regards,
> Ashok Vardharajan
>
>
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