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Add iRODS 4.3.2 #105

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merged 4 commits into from
May 7, 2024
Merged

Add iRODS 4.3.2 #105

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f14c1f8
Add iRODS 4.3.2 and samtools 1.20
kjsanger May 3, 2024
d50ee95
Do not build a container from the nightly build
kjsanger May 6, 2024
4bc04be
Fix missing client images
kjsanger May 6, 2024
90cf16d
Remove irods-dev from server images
kjsanger May 6, 2024
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93 changes: 75 additions & 18 deletions docker/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -21,20 +21,23 @@ image_names += ub-18.04-irods-4.2.11
image_names += ub-18.04-irods-4.2.12
image_names += ub-18.04-irods-4.3.0
image_names += ub-22.04-irods-4.3.1
image_names += ub-22.04-irods-4.3-nightly
image_names += ub-22.04-irods-4.3.2
# image_names += ub-22.04-irods-4.3-nightly

image_names += ub-16.04-irods-clients-dev-4.2.7
image_names += ub-18.04-irods-clients-dev-4.2.11
image_names += ub-18.04-irods-clients-dev-4.2.12
image_names += ub-18.04-irods-clients-dev-4.3.0
image_names += ub-22.04-irods-clients-dev-4.3.1
image_names += ub-22.04-irods-clients-dev-4.3-nightly
image_names += ub-22.04-irods-clients-dev-4.3.2
# image_names += ub-22.04-irods-clients-dev-4.3-nightly

image_names += ub-16.04-irods-clients-4.2.7
image_names += ub-18.04-irods-clients-4.2.11
image_names += ub-18.04-irods-clients-4.2.12
image_names += ub-22.04-irods-clients-4.3.1
image_names += ub-22.04-irods-clients-4.3-nightly
image_names += ub-22.04-irods-clients-4.3.2
# image_names += ub-22.04-irods-clients-4.3-nightly

git_url=$(shell git remote get-url origin)
git_commit=$(shell git log --pretty=format:'%H' -n 1)
Expand Down Expand Up @@ -154,6 +157,20 @@ ub-22.04-irods-4.3.1.$(TAG): irods/ubuntu/22.04/Dockerfile ub-22.04-base.$(TAG)
--tag $(DOCKER_PREFIX)/ub-22.04-irods-4.3.1:$(TAG) --file $< ./irods
touch $@

ub-22.04-irods-4.3.2.$(TAG): irods/ubuntu/22.04/Dockerfile ub-22.04-base.$(TAG)
docker buildx build $(DOCKER_ARGS) \
--load \
--build-arg BASE_IMAGE=$(DOCKER_PREFIX)/ub-22.04-base \
--build-arg IRODS_VERSION=4.3.2 \
--label org.opencontainers.image.title="iRODS 4.3.2 server, Ubuntu 22.04" \
--label org.opencontainers.image.source=$(git_url) \
--label org.opencontainers.image.revision=$(git_commit) \
--label org.opencontainers.image.version=$(TAG) \
--label org.opencontainers.image.created=$(NOW) \
--tag $(DOCKER_PREFIX)/ub-22.04-irods-4.3.2:latest \
--tag $(DOCKER_PREFIX)/ub-22.04-irods-4.3.2:$(TAG) --file $< ./irods
touch $@

ub-22.04-irods-4.3-nightly.$(TAG): irods/ubuntu/22.04/Dockerfile.nightly ub-22.04-base.$(TAG)
docker buildx build $(DOCKER_ARGS) \
--load \
Expand All @@ -177,9 +194,9 @@ ub-16.04-irods-clients-4.2.7.$(TAG): irods_clients/ubuntu/16.04/Dockerfile ub-16
--build-arg DOCKER_TAG=$(TAG) \
--build-arg IRODS_VERSION=4.2.7 \
--build-arg BATON_VERSION=4.2.1 \
--build-arg HTSLIB_VERSION=1.18 \
--build-arg SAMTOOLS_VERSION=1.18 \
--build-arg BCFTOOLS_VERSION=1.18 \
--build-arg HTSLIB_VERSION=1.20 \
--build-arg SAMTOOLS_VERSION=1.20 \
--build-arg BCFTOOLS_VERSION=1.20 \
--label org.opencontainers.image.title="iRODS 4.2.7 clients, Ubuntu 16.04" \
--label org.opencontainers.image.source=$(git_url) \
--label org.opencontainers.image.revision=$(git_commit) \
Expand All @@ -198,9 +215,9 @@ ub-18.04-irods-clients-4.2.11.$(TAG): irods_clients/ubuntu/18.04/Dockerfile ub-1
--build-arg DOCKER_TAG=$(TAG) \
--build-arg IRODS_VERSION=4.2.11 \
--build-arg BATON_VERSION=4.2.1 \
--build-arg HTSLIB_VERSION=1.18 \
--build-arg SAMTOOLS_VERSION=1.18 \
--build-arg BCFTOOLS_VERSION=1.18 \
--build-arg HTSLIB_VERSION=1.20 \
--build-arg SAMTOOLS_VERSION=1.20 \
--build-arg BCFTOOLS_VERSION=1.20 \
--label org.opencontainers.image.title="iRODS 4.2.11 clients, Ubuntu 18.04" \
--label org.opencontainers.image.source=$(git_url) \
--label org.opencontainers.image.revision=$(git_commit) \
Expand All @@ -220,9 +237,9 @@ ub-18.04-irods-clients-4.2.12.$(TAG): irods_clients/ubuntu/18.04/Dockerfile ub-1
--build-arg DOCKER_TAG=$(TAG) \
--build-arg IRODS_VERSION=4.2.12 \
--build-arg BATON_VERSION=4.2.1 \
--build-arg HTSLIB_VERSION=1.18 \
--build-arg SAMTOOLS_VERSION=1.18 \
--build-arg BCFTOOLS_VERSION=1.18 \
--build-arg HTSLIB_VERSION=1.20 \
--build-arg SAMTOOLS_VERSION=1.20 \
--build-arg BCFTOOLS_VERSION=1.20 \
--label org.opencontainers.image.title="iRODS 4.2.12 clients, Ubuntu 18.04" \
--label org.opencontainers.image.source=$(git_url) \
--label org.opencontainers.image.revision=$(git_commit) \
Expand All @@ -242,9 +259,9 @@ ub-22.04-irods-clients-4.3.1.$(TAG): irods_clients/ubuntu/22.04/Dockerfile
--build-arg DOCKER_TAG=$(TAG) \
--build-arg IRODS_VERSION=4.3.1 \
--build-arg BATON_VERSION=4.2.1 \
--build-arg HTSLIB_VERSION=1.18 \
--build-arg SAMTOOLS_VERSION=1.18 \
--build-arg BCFTOOLS_VERSION=1.18 \
--build-arg HTSLIB_VERSION=1.20 \
--build-arg SAMTOOLS_VERSION=1.20 \
--build-arg BCFTOOLS_VERSION=1.20 \
--label org.opencontainers.image.title="iRODS 4.3.1 clients, Ubuntu 22.04" \
--label org.opencontainers.image.source=$(git_url) \
--label org.opencontainers.image.revision=$(git_commit) \
Expand All @@ -254,6 +271,28 @@ ub-22.04-irods-clients-4.3.1.$(TAG): irods_clients/ubuntu/22.04/Dockerfile
--tag $(DOCKER_PREFIX)/ub-22.04-irods-clients-4.3.1:$(TAG) --file $< ./irods_clients
touch $@

ub-22.04-irods-clients-4.3.2.$(TAG): irods_clients/ubuntu/22.04/Dockerfile
docker buildx build $(DOCKER_ARGS) \
--load \
--build-context singularity=../singularity \
--build-arg DOCKER_PREFIX=$(DOCKER_PREFIX) \
--build-arg BASE_IMAGE=$(DOCKER_PREFIX)/ub-22.04-base \
--build-arg DOCKER_IMAGE=$(subst .$(TAG),,$@) \
--build-arg DOCKER_TAG=$(TAG) \
--build-arg IRODS_VERSION=4.3.2 \
--build-arg BATON_VERSION=4.2.1 \
--build-arg HTSLIB_VERSION=1.20 \
--build-arg SAMTOOLS_VERSION=1.20 \
--build-arg BCFTOOLS_VERSION=1.20 \
--label org.opencontainers.image.title="iRODS 4.3.2 clients, Ubuntu 22.04" \
--label org.opencontainers.image.source=$(git_url) \
--label org.opencontainers.image.revision=$(git_commit) \
--label org.opencontainers.image.version=$(TAG) \
--label org.opencontainers.image.created=$(NOW) \
--tag $(DOCKER_PREFIX)/ub-22.04-irods-clients-4.3.2:latest \
--tag $(DOCKER_PREFIX)/ub-22.04-irods-clients-4.3.2:$(TAG) --file $< ./irods_clients
touch $@

ub-22.04-irods-clients-4.3-nightly.$(TAG): irods_clients/ubuntu/22.04/Dockerfile.nightly
docker buildx build $(DOCKER_ARGS) \
--load \
Expand All @@ -264,9 +303,9 @@ ub-22.04-irods-clients-4.3-nightly.$(TAG): irods_clients/ubuntu/22.04/Dockerfile
--build-arg DOCKER_TAG=$(TAG) \
--build-arg IRODS_VERSION=4.3-nightly \
--build-arg BATON_VERSION=4.2.1 \
--build-arg HTSLIB_VERSION=1.18 \
--build-arg SAMTOOLS_VERSION=1.18 \
--build-arg BCFTOOLS_VERSION=1.18 \
--build-arg HTSLIB_VERSION=1.20 \
--build-arg SAMTOOLS_VERSION=1.20 \
--build-arg BCFTOOLS_VERSION=1.20 \
--label org.opencontainers.image.title="iRODS 4.3-nightly clients, Ubuntu 22.04" \
--label org.opencontainers.image.source=$(git_url) \
--label org.opencontainers.image.revision=$(git_commit) \
Expand Down Expand Up @@ -362,6 +401,24 @@ ub-22.04-irods-clients-dev-4.3.1.$(TAG): irods_clients_dev/ubuntu/22.04/Dockerfi
--tag $(DOCKER_PREFIX)/ub-22.04-irods-clients-dev-4.3.1:$(TAG) --file $< ./irods_clients_dev
touch $@

ub-22.04-irods-clients-dev-4.3.2.$(TAG): irods_clients_dev/ubuntu/22.04/Dockerfile
docker buildx build $(DOCKER_ARGS) \
--load \
--build-context singularity=../singularity \
--build-arg DOCKER_PREFIX=$(DOCKER_PREFIX) \
--build-arg BASE_IMAGE=ubuntu:22.04 \
--build-arg IRODS_VERSION=4.3.2 \
--build-arg DOCKER_IMAGE=$(subst .$(TAG),,$@) \
--build-arg DOCKER_TAG=$(TAG) \
--label org.opencontainers.image.title="iRODS 4.3.2 client development, Ubuntu 22.04" \
--label org.opencontainers.image.source=$(git_url) \
--label org.opencontainers.image.revision=$(git_commit) \
--label org.opencontainers.image.version=$(TAG) \
--label org.opencontainers.image.created=$(NOW) \
--tag $(DOCKER_PREFIX)/ub-22.04-irods-clients-dev-4.3.2:latest \
--tag $(DOCKER_PREFIX)/ub-22.04-irods-clients-dev-4.3.2:$(TAG) --file $< ./irods_clients_dev
touch $@

ub-22.04-irods-clients-dev-4.3-nightly.$(TAG): irods_clients_dev/ubuntu/22.04/Dockerfile.nightly
docker buildx build $(DOCKER_ARGS) \
--load \
Expand Down
4 changes: 4 additions & 0 deletions docker/irods/scripts/configure_irods.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,10 @@ case "$IRODS_VERSION" in
# Logging has been changed to use rsyslog. A potential enhancement is to configure that here.
python3 /var/lib/irods/scripts/setup_irods.py < /opt/docker/irods/config/4.3.x.setup_irods.py.in
;;
4.3.2)
# Logging has been changed to use rsyslog. A potential enhancement is to configure that here.
python3 /var/lib/irods/scripts/setup_irods.py < /opt/docker/irods/config/4.3.x.setup_irods.py.in
;;
*)
echo Unknown iRODS version "$IRODS_VERSION"
exit 1
Expand Down
3 changes: 1 addition & 2 deletions docker/irods/ubuntu/16.04/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -39,8 +39,7 @@ RUN curl -sSL https://packages.irods.org/irods-signing-key.asc | apt-key add - &
irods-server="$IRODS_VERSION" \
irods-runtime="$IRODS_VERSION" \
irods-database-plugin-postgres="$IRODS_VERSION" \
irods-icommands="$IRODS_VERSION" \
irods-dev="$IRODS_VERSION" && \
irods-icommands="$IRODS_VERSION" && \
apt-get install -q -y -f && \
unattended-upgrade -v && \
apt-get remove -q -y unattended-upgrades && \
Expand Down
3 changes: 1 addition & 2 deletions docker/irods/ubuntu/18.04/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -43,8 +43,7 @@ RUN curl -sSL https://packages.irods.org/irods-signing-key.asc | apt-key add - &
irods-server="${IRODS_VERSION}-${IRODS_REVISION}~$(lsb_release -sc)" \
irods-runtime="${IRODS_VERSION}-${IRODS_REVISION}~$(lsb_release -sc)" \
irods-database-plugin-postgres="${IRODS_VERSION}-${IRODS_REVISION}~$(lsb_release -sc)" \
irods-icommands="${IRODS_VERSION}-${IRODS_REVISION}~$(lsb_release -sc)" \
irods-dev="${IRODS_VERSION}-${IRODS_REVISION}~$(lsb_release -sc)" && \
irods-icommands="${IRODS_VERSION}-${IRODS_REVISION}~$(lsb_release -sc)" && \
apt-get install -q -y -f && \
unattended-upgrade -v && \
apt-get remove -q -y unattended-upgrades && \
Expand Down
3 changes: 1 addition & 2 deletions docker/irods/ubuntu/22.04/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -43,8 +43,7 @@ RUN curl -sSL https://packages.irods.org/irods-signing-key.asc | apt-key add - &
irods-server="${IRODS_VERSION}-${IRODS_REVISION}~$(lsb_release -sc)" \
irods-runtime="${IRODS_VERSION}-${IRODS_REVISION}~$(lsb_release -sc)" \
irods-database-plugin-postgres="${IRODS_VERSION}-${IRODS_REVISION}~$(lsb_release -sc)" \
irods-icommands="${IRODS_VERSION}-${IRODS_REVISION}~$(lsb_release -sc)" \
irods-dev="${IRODS_VERSION}-${IRODS_REVISION}~$(lsb_release -sc)" && \
irods-icommands="${IRODS_VERSION}-${IRODS_REVISION}~$(lsb_release -sc)" && \
apt-get install -q -y -f && \
unattended-upgrade -v && \
apt-get remove -q -y unattended-upgrades && \
Expand Down