Hi All
I have recently started learning the Galaxy setup starting with an upgrade. Made some headway but I was wondering if someone could comment on a problem that has emerged. The system is a Galaxy 18.05 installation (upgraded from 17.01) on an Altair PBS scheduler with drmaa setup (working)
Conda problem: Failed to activate conda environment.
Conda works during tool installation or reinstallation.
Galaxy tools have been updated/reinstalled so they all look "green" in manage tools.
In Manage Dependencies there are a number of "Dependency resolved but version not found" warnings, otherwise the deps look clean.
When running tools in Galaxy errors occur, after the jobs have correctly deployed on the cluster.
The galaxy application raised errors like the two below.
"Failed to activate conda environment! Error was: Fatal Python error: Py_Initialize: Unable to get the locale encoding File "/home/.galaxy/tooldeps/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodings/__init__.py", line 123 raise C"
"
Failed to activate conda environment! Error was: CondaEnvironmentError: Environment error: Cannot activate environment bash. User does not have write access for conda symlinks.
"
Galaxy started and stopped using supervisord with config below:
Thanks, hopefully someone has seen this before ...
regards, Gerhard
[program:web] command = uwsgi --plugin python --virtualenv /home/.galaxy/.venv --ini-paste /home/.galaxy/config/galaxy.ini directory = /home/.galaxy umask = 022 autostart = true autorestart = true startsecs = 10 user = galaxy numprocs = 1 stopsignal = INT
[program:handler] command = python ./scripts/galaxy-main -c /home/.galaxy/config/galaxy.ini --server-name=handler%(process_num)s directory = /home/.galaxy process_name = handler%(process_num)s numprocs = 1 umask = 022 autostart = true autorestart = true startsecs = 10 user = galaxy environment = VIRTUAL_ENV="/home/.galaxy/.venv",PATH="/home/.galaxy/.venv/bin:%(ENV_PATH)s",http_proxy="http://storage2.eth.hpc:3128/%22,https_proxy=%22http://storage2.eth.hpc:3128..." stdout_logfile = /home/.galaxy/handler%(process_num)s.log redirect_stderr = true
[group:galaxy] programs = handler, web
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