diff --git a/.github/workflows/single.sh b/.github/workflows/single.sh index 446d867ae..7a51314da 100755 --- a/.github/workflows/single.sh +++ b/.github/workflows/single.sh @@ -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 "$WORKING_DIR/" diff --git a/compose/base-images/galaxy-container-base/Dockerfile b/compose/base-images/galaxy-container-base/Dockerfile index 6cf33a516..b0d0d4674 100644 --- a/compose/base-images/galaxy-container-base/Dockerfile +++ b/compose/base-images/galaxy-container-base/Dockerfile @@ -3,7 +3,7 @@ FROM buildpack-deps:20.04 as build_singularity COPY ./files/common_cleanup.sh /usr/bin/common_cleanup.sh # Install Go (only needed for building singularity) -ENV GO_VERSION=1.13 +ENV GO_VERSION=1.16 RUN apt update && apt install --no-install-recommends cryptsetup-bin uuid-dev -y \ && wget https://dl.google.com/go/go${GO_VERSION}.linux-amd64.tar.gz \ && tar -C /usr/local -xzvf go${GO_VERSION}.linux-amd64.tar.gz \ @@ -11,9 +11,10 @@ RUN apt update && apt install --no-install-recommends cryptsetup-bin uuid-dev -y && /usr/bin/common_cleanup.sh ENV PATH=/usr/local/go/bin:${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-${SINGULARITY_VERSION} singularity \ && cd singularity \ && ./mconfig \ && make -C builddir \ diff --git a/compose/galaxy-server/Dockerfile b/compose/galaxy-server/Dockerfile index d789c2250..667683655 100644 --- a/compose/galaxy-server/Dockerfile +++ b/compose/galaxy-server/Dockerfile @@ -50,7 +50,7 @@ RUN curl -s -L "https://repo.anaconda.com/miniconda/Miniconda3-${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 @@ -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=$EXPORT_DIR/galaxy \ diff --git a/compose/tests/galaxy-bioblend-test/Dockerfile b/compose/tests/galaxy-bioblend-test/Dockerfile index a635b421c..c7968fd04 100644 --- a/compose/tests/galaxy-bioblend-test/Dockerfile +++ b/compose/tests/galaxy-bioblend-test/Dockerfile @@ -1,6 +1,6 @@ FROM alpine:3.11 as build -ENV BIOBLEND_VERSION=0.13.0 +ENV BIOBLEND_VERSION=0.16.0 ADD "https://github.com/galaxyproject/bioblend/archive/v$BIOBLEND_VERSION.zip" /src/bioblend.zip RUN apk update && apk add curl python3-dev unzip \ diff --git a/compose/tests/galaxy-selenium-test/Dockerfile b/compose/tests/galaxy-selenium-test/Dockerfile index 370264852..bed644eae 100644 --- a/compose/tests/galaxy-selenium-test/Dockerfile +++ b/compose/tests/galaxy-selenium-test/Dockerfile @@ -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 diff --git a/galaxy/Dockerfile b/galaxy/Dockerfile index ffe96856e..db6735164 100644 --- a/galaxy/Dockerfile +++ b/galaxy/Dockerfile @@ -16,7 +16,7 @@ MAINTAINER Björn A. Grüning, bjoern.gruening@gmail.com 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 \