I would like to change the middle panel of the galaxy Galaxy docker instance in the "flavor" I am working on and is provided through quay.io. I was wondering what the best way is to do this, since I would like to do this without the /export directory. The things I tried are:
Thank you in advance
I want to propose a docker galaxy stable with some tools available on the toolshed for a project. I had a working version in September but when I added a new tool in December an error appeared.
py35 inst: /home/galaxy/bioblend-master/.tox/.tmp/package/1/bioblend-0.14.0.zip ERROR: invocation failed (exit code 1), logfile: /home/galaxy/bioblend-master/.tox/py35/log/py35-2.log ================================== log start =================================== DEPRECATION: Python 3.5 reached the end of its life on September 13th, 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove support for this functionality. Processing ./.tox/.tmp/package/1/bioblend-0.14.0.zip ERROR: Package 'bioblend' requires a different Python: 3.5.2 not in '>=3.6' =================================== log end ==================================== ___________________________________ summary ____________________________________ ERROR: py35: InvocationError for command /home/galaxy/bioblend-master/.tox/py35/bin/python -m pip install --exists-action w .tox/.tmp/package/1/bioblend-0.14.0.zip (exited with code 1)
So I upgraded the version of python to 3.6 in my .travis.yml file :
python: 3.6 env: - TOX_ENV=py36
But now I have this error:
py36 create: /home/galaxy/bioblend-master/.tox/py36 ERROR: InterpreterNotFound: python3.6 ___________________________________ summary ____________________________________ ERROR: py36: InterpreterNotFound: python3.6 Makefile:63: recipe for target 'test_bioblend' failed make: *** [test_bioblend] Error 1 The command "make test_bioblend" exited with 2.
I also tried with python 3.7. I don't understand why he can't find the interpreter anymore. Any ideas ?
Thank you in advance
bgruening/galaxy-stableimage and it works fine in my local machine.. I can install a tool from toolshed and use it. However, when I installed it in a server and run it with docker, tool installation is not complete, I get "Conda dependency seemingly installed but failed to build job environment." error. I did everything same in both computers but couldn't figure out the problem. I guess it's permission issue at server but don't know how to debug it.
-su: /usr/lib/postgresql/11/bin/initdb: No such file or directory sed: can't read /etc/postgresql/11/main/postgresql.conf: No such file or directory postgresql: unrecognized service -su: psql: command not found -su: createdb: command not found postgresql: unrecognized service postgresql: unrecognized service
git submodule update --init --recursive. Sorry for the noise.
hello, I have a question about galaxy+docker. I'm building an image on top of bgruening. I successfully added my some public (devteam) tools, plus my own tools. In the dockerfile I execute RUN install_tool_deps -v -u $GALAXY_DEFAULT_ADMIN_USER -p $GALAXY_DEFAULT_ADMIN_PASSWORD -g http://localhost:8080 -t /data/local_tool_conf.xml, it seems to be working. It shows progress while installing all dependencies in mulled conda environments.
Then, I start a container. Log in as admin, under Dependencies I see that all my tools have the green flag, dependencies are met. The mulled environments are physically there. When I try to launch a tool, though, it returns an error, saying "Not a conda environment", and showing me the path of the mulled environment. Observations:
the path shown in the error is correct
if I bash inside the container, I can activate the environment, and the tool works ok if launched from the command line.
docker file: https://pastebin.com/5SD4AJ1B
some more interesting elements:
install_tool_depsinstruction from the dockerfile, and I run it in a container afterwards, it complains about permissions, and suggests to chown -R 1450:1450 /tool_deps/_conda/pkgs/cache
chown -R 1450:1450 /tool_deps/_conda/pkgs/cachethen install_tool_deps starts working fine, and the environments it creates (identical to the non-working ones from before), work fine.
I would say this is a permissions issue. Somehow the mulled environments -which are installed after the startup-lite instruction, are not available to the galaxy user 'admin' for activation.
install_tool_depsneeds a running server in order to work. Ideas?
USER rootwhere you need docker to switch back to acting as root?
install_tool_depsneeds to be run as
galaxyuser in order to create the envs with the correct ownership
install_tool_depsalso needs a running
startup_litein order to work, a galaxy server at localhost:8080 must be alive somehow.
startup_liteneeds to be launched while acting as root, otherwise it gets stuck on 'waiting for database'
install_tool_depswhile a galaxy server is alive
chgrp -R galaxy /tool_deps/_conda/envs && chmod g+s -R /tool_deps/_conda/envsjust after
startup_lite. This way, all the envs that will be placed in that folder will inherit the
galaxygroup ownership. Running
chmod/chuserafter the installation of all the dependencies would have worked as well, but it would be excruciatingly long.