Re: [galaxy-dev] Conda problems: Failed to activate conda environment

[Björn Grüning]

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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[galaxy-dev] Conda problems: Failed to activate conda environment

[Van Wageningen, GERHARD [gerha...@sun.ac.za]]

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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The integrity and confidentiality of this email is governed by these terms. 
Disclaimer
Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende 
bepalings gereël. Vrywaringsklousule
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

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  http://galaxyproject.org/search/