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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