:whale::bar_chart::books: Docker Images tracking the stable Galaxy releases.
Hello everyone,
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:
- manipulating the
/galaxy-central/static/welcome.htmlfile - changing the welcome_url in
/etc/galaxy/galaxy.yml
Both things did not affect the middle panel ....
Thank you in advance
Are there people with experience using the galaxy docker image on MacOS? It seems that cvmfs is not working if the --privileged tag is used, while the same containers works perfectly on linux/windows. Are there additional steps that have to be taken to make this work on MacOS?
Thank you in advance
Hi everyone,
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 Please upgrade your Python as Python 3.5 is no longer maintained.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=py36But 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-stable image 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.
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
`
-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:
- all the tools installed from the standard toolshed work fine. No problems there, their environments are recognized as such.
- if I exclude the
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 - If I actually execute
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_deps needs a running server in order to work. Ideas?
USER root where you need docker to switch back to acting as root?
install_tool_depsneeds to be run asgalaxyuser in order to create the envs with the correct ownershipinstall_tool_depsalso needs a runningstartup_litein order to work, a galaxy server at localhost:8080 must be alive somehow.- Unfortunately,
startup_liteneeds to be launched while acting as root, otherwise it gets stuck on 'waiting for database'
install_tool_deps while a galaxy server is alive
chgrp -R galaxy /tool_deps/_conda/envs && chmod g+s -R /tool_deps/_conda/envs just after startup_lite. This way, all the envs that will be placed in that folder will inherit the galaxy group ownership. Running chmod/chuser after the installation of all the dependencies would have worked as well, but it would be excruciatingly long.
seems to be causing an issue : bgruening/docker-galaxy-stable#588
is it possible we are supposed to use the other one: https://wheels.galaxyproject.org/simple/futures/futures-3.1.1-py2-none-any.whl
can we add a condition in the file requirements.txt to determine when to use eachpackage?
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