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Bump to 22.05 #600

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979dee7
upgrade to 21.01
bgruening Apr 18, 2021
50bf6f1
* bumped version to 21.09
chambm Dec 15, 2021
b8059e9
* updated singularity version (it's now singularity-ce)
chambm Dec 15, 2021
513061b
* fixed singularity tarball url and extracted directory
chambm Dec 15, 2021
c025b85
* upgraded Go version
chambm Dec 15, 2021
e297ad6
update bioblend version
bgruening Jan 1, 2022
25e96c4
rebuild selenium test image
bgruening Jan 1, 2022
62ec390
Blindly updating to 22.05 and crossing fingers
chambm Mar 22, 2023
cbec822
Update Dockerfile to 22.05
chambm Mar 22, 2023
2558d1d
Update Dockerfile to 22.05
chambm Mar 22, 2023
7f64eee
Enable ssh-rsa
chambm Mar 22, 2023
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2 changes: 1 addition & 1 deletion .github/workflows/single.sh
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Expand Up @@ -107,7 +107,7 @@ docker_exec bash -c "cvmfs_config chksetup"
docker_exec bash -c "ls /cvmfs/data.galaxyproject.org/byhand"

# Test SFTP Server
sshpass -p $GALAXY_USER_PASSWD sftp -v -P 8022 -o User=$GALAXY_USER -o "StrictHostKeyChecking no" localhost <<< $'put time.txt'
sshpass -p $GALAXY_USER_PASSWD sftp -v -P 8022 -o User=$GALAXY_USER -o "StrictHostKeyChecking no" -O "HostKeyAlgorithms=+ssh-rsa" localhost <<< $'put time.txt'

# Run a ton of BioBlend test against our servers.
cd "$WORKING_DIR/test/bioblend/" && . ./test.sh && cd "$WORKING_DIR/"
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9 changes: 5 additions & 4 deletions compose/base-images/galaxy-container-base/Dockerfile
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Expand Up @@ -3,17 +3,18 @@ FROM buildpack-deps:20.04 as build_singularity
COPY ./files/common_cleanup.sh /usr/bin/common_cleanup.sh

# Install Go (only needed for building singularity)
ENV GO_VERSION=1.13
ENV GO_VERSION=1.16
RUN apt update && apt install --no-install-recommends cryptsetup-bin uuid-dev -y \
&& wget https://dl.google.com/go/go${GO_VERSION}.linux-amd64.tar.gz \
&& tar -C /usr/local -xzvf go${GO_VERSION}.linux-amd64.tar.gz \
&& rm go${GO_VERSION}.linux-amd64.tar.gz \
&& /usr/bin/common_cleanup.sh

ENV PATH=/usr/local/go/bin:${PATH}
ENV SINGULARITY_VERSION=3.5.3
RUN wget https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-${SINGULARITY_VERSION}.tar.gz \
&& tar -xzf singularity-${SINGULARITY_VERSION}.tar.gz \
ENV SINGULARITY_VERSION=3.9.2
RUN wget https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-ce-${SINGULARITY_VERSION}.tar.gz \
&& tar -xzf singularity-ce-${SINGULARITY_VERSION}.tar.gz \
&& mv singularity-ce-${SINGULARITY_VERSION} singularity \
&& cd singularity \
&& ./mconfig \
&& make -C builddir \
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4 changes: 2 additions & 2 deletions compose/galaxy-server/Dockerfile
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Expand Up @@ -50,7 +50,7 @@ RUN curl -s -L "https://repo.anaconda.com/miniconda/Miniconda3-${MINICONDA_VERSI

FROM build_base as build_galaxy

ARG GALAXY_RELEASE=release_20.09
ARG GALAXY_RELEASE=release_22.05
ARG GALAXY_REPO=https://github.com/galaxyproject/galaxy

COPY ./files/common_cleanup.sh /usr/bin/common_cleanup.sh
Expand Down Expand Up @@ -83,7 +83,7 @@ ENV EXPORT_DIR=/export \
GALAXY_PYTHON=/usr/bin/python3 \
HTCONDOR_ROOT=/opt/htcondor

ENV GALAXY_RELEASE=${GALAXY_RELEASE:-release_20.09} \
ENV GALAXY_RELEASE=${GALAXY_RELEASE:-release_22.05} \
GALAXY_REPO=${GALAXY_REPO:-https://github.com/galaxyproject/galaxy} \
GALAXY_STATIC_DIR=$GALAXY_ROOT/static \
GALAXY_EXPORT=$EXPORT_DIR/galaxy \
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2 changes: 1 addition & 1 deletion compose/tests/galaxy-bioblend-test/Dockerfile
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@@ -1,6 +1,6 @@
FROM alpine:3.11 as build

ENV BIOBLEND_VERSION=0.13.0
ENV BIOBLEND_VERSION=0.16.0

ADD "https://github.com/galaxyproject/bioblend/archive/v$BIOBLEND_VERSION.zip" /src/bioblend.zip
RUN apk update && apk add curl python3-dev unzip \
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2 changes: 1 addition & 1 deletion compose/tests/galaxy-selenium-test/Dockerfile
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@@ -1,6 +1,6 @@
FROM selenium/standalone-chrome:3.141.59

ARG GALAXY_RELEASE=release_20.09
ARG GALAXY_RELEASE=release_22.05
ARG GALAXY_REPO=https://github.com/galaxyproject/galaxy

ENV GALAXY_ROOT=/galaxy
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11 changes: 6 additions & 5 deletions galaxy/Dockerfile
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Expand Up @@ -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 \
Expand Down Expand Up @@ -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 \
Expand Down Expand Up @@ -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 \
Expand Down Expand Up @@ -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/ \
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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.

# cleanup dance
&& find $GALAXY_ROOT/ -name '*.pyc' -delete | true \
&& find /usr/lib/ -name '*.pyc' -delete | true \
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