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