Merge pull request #105 from kjsanger/feature/irods-4.3.2

Add iRODS 4.3.2
wtsi-npg · May 7, 2024 · a70b34f · a70b34f
2 parents 01bf413 + 90cf16d
commit a70b34f
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Showing 5 changed files with 82 additions and 24 deletions.
diff --git a/docker/Makefile b/docker/Makefile
@@ -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)
@@ -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 $(DOCKER_ARGS) \
 	--load \
@@ -177,9 +194,9 @@ ub-16.04-irods-clients-4.2.7.$(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=$(git_commit) \
@@ -198,9 +215,9 @@ ub-18.04-irods-clients-4.2.11.$(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=$(git_commit) \
@@ -220,9 +237,9 @@ ub-18.04-irods-clients-4.2.12.$(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=$(git_commit) \
@@ -242,9 +259,9 @@ ub-22.04-irods-clients-4.3.1.$(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=$(git_commit) \
@@ -254,6 +271,28 @@ ub-22.04-irods-clients-4.3.1.$(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 $(DOCKER_ARGS) \
 	--load \
@@ -264,9 +303,9 @@ ub-22.04-irods-clients-4.3-nightly.$(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=$(git_commit) \
@@ -362,6 +401,24 @@ ub-22.04-irods-clients-dev-4.3.1.$(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 \

diff --git a/docker/irods/scripts/configure_irods.sh b/docker/irods/scripts/configure_irods.sh
@@ -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

diff --git a/docker/irods/ubuntu/16.04/Dockerfile b/docker/irods/ubuntu/16.04/Dockerfile
@@ -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 && \

diff --git a/docker/irods/ubuntu/18.04/Dockerfile b/docker/irods/ubuntu/18.04/Dockerfile
@@ -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 && \

diff --git a/docker/irods/ubuntu/22.04/Dockerfile b/docker/irods/ubuntu/22.04/Dockerfile
@@ -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 && \