Hi Gerhard,
it seems your tool is picking up the old tool_dependency version and not
the conda version of python.
Have a look at
https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample
to configure the order of dependency resolution in Galaxy.
Cheers,
Bjoern
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/",https_proxy="http://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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