-
Notifications
You must be signed in to change notification settings - Fork 133
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Bump to 22.05 #600
Open
chambm
wants to merge
11
commits into
bgruening:master
Choose a base branch
from
chambm:22.05
base: master
Could not load branches
Branch not found: {{ refName }}
Loading
Could not load tags
Nothing to show
Loading
Are you sure you want to change the base?
Some commits from the old base branch may be removed from the timeline,
and old review comments may become outdated.
Open
Bump to 22.05 #600
Changes from all commits
Commits
Show all changes
11 commits
Select commit
Hold shift + click to select a range
979dee7
upgrade to 21.01
bgruening 50bf6f1
* bumped version to 21.09
chambm b8059e9
* updated singularity version (it's now singularity-ce)
chambm 513061b
* fixed singularity tarball url and extracted directory
chambm c025b85
* upgraded Go version
chambm e297ad6
update bioblend version
bgruening 25e96c4
rebuild selenium test image
bgruening 62ec390
Blindly updating to 22.05 and crossing fingers
chambm cbec822
Update Dockerfile to 22.05
chambm 2558d1d
Update Dockerfile to 22.05
chambm 7f64eee
Enable ssh-rsa
chambm File filter
Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
|
@@ -16,7 +16,7 @@ MAINTAINER Björn A. Grüning, [email protected] | |
ARG GALAXY_RELEASE | ||
ARG GALAXY_REPO | ||
|
||
ENV GALAXY_RELEASE=${GALAXY_RELEASE:-release_20.09} \ | ||
ENV GALAXY_RELEASE=${GALAXY_RELEASE:-release_22.05} \ | ||
GALAXY_REPO=${GALAXY_REPO:-https://github.com/galaxyproject/galaxy} \ | ||
GALAXY_ROOT=/galaxy-central \ | ||
GALAXY_CONFIG_DIR=/etc/galaxy \ | ||
|
@@ -139,11 +139,12 @@ RUN curl -s -L https://repo.anaconda.com/miniconda/Miniconda3-4.7.10-Linux-x86_6 | |
|
||
|
||
RUN cp $GALAXY_HOME/.bashrc ~/ | ||
RUN mkdir $GALAXY_ROOT \ | ||
&& curl -L -s $GALAXY_REPO/archive/$GALAXY_RELEASE.tar.gz | tar xzf - --strip-components=1 -C $GALAXY_ROOT \ | ||
RUN curl -L -s $GALAXY_REPO/tarball/$GALAXY_RELEASE | tar xzf - -C / \ | ||
&& ln -s /galaxyproject-galaxy-* $GALAXY_ROOT \ | ||
&& PATH=$GALAXY_CONDA_PREFIX/bin/:$PATH virtualenv $GALAXY_VIRTUAL_ENV \ | ||
&& chown -R $GALAXY_USER:$GALAXY_USER $GALAXY_VIRTUAL_ENV \ | ||
&& chown -R $GALAXY_USER:$GALAXY_USER $GALAXY_ROOT \ | ||
&& chown -R $GALAXY_USER:$GALAXY_USER /galaxyproject-galaxy-* \ | ||
# Setup Galaxy configuration files. | ||
&& mkdir -p $GALAXY_CONFIG_DIR $GALAXY_CONFIG_DIR/web \ | ||
&& chown -R $GALAXY_USER:$GALAXY_USER $GALAXY_CONFIG_DIR \ | ||
|
@@ -186,7 +187,7 @@ RUN mkdir -p /shed_tools $EXPORT_DIR/ftp/ \ | |
&& ln -s /tool_deps/ $EXPORT_DIR/tool_deps \ | ||
# Configure Galaxy to use the Tool Shed | ||
&& chown $GALAXY_USER:$GALAXY_USER $EXPORT_DIR/tool_deps \ | ||
&& apt update -qq && apt install --no-install-recommends -y ansible \ | ||
&& apt update -qq && apt install --no-install-recommends -y ansible g++ make \ | ||
&& ansible-playbook /ansible/provision.yml \ | ||
--extra-vars galaxy_venv_dir=$GALAXY_VIRTUAL_ENV \ | ||
--extra-vars galaxy_log_dir=$GALAXY_LOGS_DIR \ | ||
|
@@ -222,7 +223,7 @@ RUN mkdir -p /shed_tools $EXPORT_DIR/ftp/ \ | |
&& python /usr/local/bin/setup_postgresql.py --dbuser galaxy --dbpassword galaxy --db-name galaxy --dbpath $PG_DATA_DIR_DEFAULT --dbversion $PG_VERSION \ | ||
&& service postgresql start \ | ||
&& service postgresql stop \ | ||
&& apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && rm -rf ~/.cache/ \ | ||
&& apt-get autoremove -y make g++ gcc && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && rm -rf ~/.cache/ \ | ||
# cleanup dance | ||
&& find $GALAXY_ROOT/ -name '*.pyc' -delete | true \ | ||
&& find /usr/lib/ -name '*.pyc' -delete | true \ | ||
|
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
It looks like pysam is expecting
make
(and likely gcc) to exist still. Although I would have expected the Galaxy environment to have a precompiled build of pysam already.