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Add iRODS 4.3.3 and remove iRODS 4.3.0 #112

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103 changes: 64 additions & 39 deletions docker/Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -19,24 +19,28 @@ image_names := ub-16.04-base ub-18.04-base ub-22.04-base
image_names += ub-16.04-irods-4.2.7
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-4.3.2
image_names += ub-22.04-irods-4.3.3
# 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-4.3.2
image_names += ub-22.04-irods-clients-dev-4.3.3
# 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-4.3.2
image_names += ub-22.04-irods-clients-4.3.3
# image_names += ub-22.04-irods-clients-4.3-nightly

git_url=$(shell git remote get-url origin)
Expand Down Expand Up @@ -135,21 +139,6 @@ ub-18.04-irods-4.2.12.$(TAG): irods/ubuntu/18.04/Dockerfile ub-18.04-base.$(TAG)
--tag $(DOCKER_PREFIX)/ub-18.04-irods-4.2.12:$(TAG) --file $< ./irods
touch $@

ub-18.04-irods-4.3.0.$(TAG): irods/ubuntu/18.04/Dockerfile ub-18.04-base.$(TAG)
docker buildx build $(DOCKER_ARGS) \
--load \
--build-arg BASE_IMAGE=$(DOCKER_PREFIX)/ub-18.04-base \
--build-arg IRODS_VERSION=4.3.0 \
--label org.opencontainers.image.title="iRODS 4.3.0 server, Ubuntu 18.04" \
--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) \
--label org.opencontainers.image.vendor=npg.sanger.ac.uk \
--tag $(DOCKER_PREFIX)/ub-18.04-irods-4.3.0:latest \
--tag $(DOCKER_PREFIX)/ub-18.04-irods-4.3.0:$(TAG) --file $< ./irods
touch $@

ub-22.04-irods-4.3.1.$(TAG): irods/ubuntu/22.04/Dockerfile ub-22.04-base.$(TAG)
docker buildx build $(DOCKER_ARGS) \
--load \
Expand Down Expand Up @@ -180,6 +169,20 @@ ub-22.04-irods-4.3.2.$(TAG): irods/ubuntu/22.04/Dockerfile ub-22.04-base.$(TAG)
--tag $(DOCKER_PREFIX)/ub-22.04-irods-4.3.2:$(TAG) --file $< ./irods
touch $@

ub-22.04-irods-4.3.3.$(TAG): irods/ubuntu/22.04/Dockerfile ub-22.04-base.$(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 4.3.3 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-4.3.3:latest \
--tag $(DOCKER_PREFIX)/ub-22.04-irods-4.3.3:$(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 $(DOCKER_ARGS) \
--load \
Expand All @@ -203,7 +206,7 @@ ub-16.04-irods-clients-4.2.7.$(TAG): irods_clients/ubuntu/16.04/Dockerfile ub-16
--build-arg DOCKER_IMAGE=$(subst .$(TAG),,$@) \
--build-arg DOCKER_TAG=$(TAG) \
--build-arg IRODS_VERSION=4.2.7 \
--build-arg BATON_VERSION=4.2.1 \
--build-arg BATON_VERSION=4.2.2 \
--build-arg HTSLIB_VERSION=1.20 \
--build-arg SAMTOOLS_VERSION=1.20 \
--build-arg BCFTOOLS_VERSION=1.20 \
Expand All @@ -225,7 +228,7 @@ ub-18.04-irods-clients-4.2.11.$(TAG): irods_clients/ubuntu/18.04/Dockerfile ub-1
--build-arg DOCKER_IMAGE=$(subst .$(TAG),,$@) \
--build-arg DOCKER_TAG=$(TAG) \
--build-arg IRODS_VERSION=4.2.11 \
--build-arg BATON_VERSION=4.2.1 \
--build-arg BATON_VERSION=4.2.2 \
--build-arg HTSLIB_VERSION=1.20 \
--build-arg SAMTOOLS_VERSION=1.20 \
--build-arg BCFTOOLS_VERSION=1.20 \
Expand Down Expand Up @@ -271,7 +274,7 @@ ub-22.04-irods-clients-4.3.1.$(TAG): irods_clients/ubuntu/22.04/Dockerfile
--build-arg DOCKER_IMAGE=$(subst .$(TAG),,$@) \
--build-arg DOCKER_TAG=$(TAG) \
--build-arg IRODS_VERSION=4.3.1 \
--build-arg BATON_VERSION=4.2.1 \
--build-arg BATON_VERSION=4.2.2 \
--build-arg HTSLIB_VERSION=1.20 \
--build-arg SAMTOOLS_VERSION=1.20 \
--build-arg BCFTOOLS_VERSION=1.20 \
Expand All @@ -294,7 +297,7 @@ ub-22.04-irods-clients-4.3.2.$(TAG): irods_clients/ubuntu/22.04/Dockerfile
--build-arg DOCKER_IMAGE=$(subst .$(TAG),,$@) \
--build-arg DOCKER_TAG=$(TAG) \
--build-arg IRODS_VERSION=4.3.2 \
--build-arg BATON_VERSION=4.2.1 \
--build-arg BATON_VERSION=4.2.2 \
--build-arg HTSLIB_VERSION=1.20 \
--build-arg SAMTOOLS_VERSION=1.20 \
--build-arg BCFTOOLS_VERSION=1.20 \
Expand All @@ -308,6 +311,28 @@ ub-22.04-irods-clients-4.3.2.$(TAG): irods_clients/ubuntu/22.04/Dockerfile
--tag $(DOCKER_PREFIX)/ub-22.04-irods-clients-4.3.2:$(TAG) --file $< ./irods_clients
touch $@

ub-22.04-irods-clients-4.3.3.$(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=$(TAG) \
--build-arg IRODS_VERSION=4.3.3 \
--build-arg BATON_VERSION=4.2.2 \
--build-arg HTSLIB_VERSION=1.20 \
--build-arg SAMTOOLS_VERSION=1.20 \
--build-arg BCFTOOLS_VERSION=1.20 \
--label org.opencontainers.image.title="iRODS 4.3.3 clients, Ubuntu 22.04" \
--label org.opencontainers.image.source=$(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-4.3.3:latest \
--tag $(DOCKER_PREFIX)/ub-22.04-irods-clients-4.3.3:$(TAG) --file $< ./irods_clients
touch $@

ub-22.04-irods-clients-4.3-nightly.$(TAG): irods_clients/ubuntu/22.04/Dockerfile.nightly
docker buildx build $(DOCKER_ARGS) \
--load \
Expand All @@ -317,7 +342,7 @@ ub-22.04-irods-clients-4.3-nightly.$(TAG): irods_clients/ubuntu/22.04/Dockerfile
--build-arg DOCKER_IMAGE=$(subst .$(TAG),,$@) \
--build-arg DOCKER_TAG=$(TAG) \
--build-arg IRODS_VERSION=4.3-nightly \
--build-arg BATON_VERSION=4.2.1 \
--build-arg BATON_VERSION=4.2.2 \
--build-arg HTSLIB_VERSION=1.20 \
--build-arg SAMTOOLS_VERSION=1.20 \
--build-arg BCFTOOLS_VERSION=1.20 \
Expand Down Expand Up @@ -385,60 +410,60 @@ ub-18.04-irods-clients-dev-4.2.12.$(TAG): irods_clients_dev/ubuntu/18.04/Dockerf
--tag $(DOCKER_PREFIX)/ub-18.04-irods-clients-dev-4.2.12:$(TAG) --file $< ./irods_clients_dev
touch $@

ub-18.04-irods-clients-dev-4.3.0.$(TAG): irods_clients_dev/ubuntu/18.04/Dockerfile
ub-22.04-irods-clients-dev-4.3.1.$(TAG): irods_clients_dev/ubuntu/22.04/Dockerfile
docker buildx build $(DOCKER_ARGS) \
--load \
--build-context singularity=../singularity \
--build-arg BASE_IMAGE=ubuntu:18.04 \
--build-arg DOCKER_PREFIX=$(DOCKER_PREFIX) \
--build-arg BASE_IMAGE=ubuntu:22.04 \
--build-arg IRODS_VERSION=4.3.1 \
--build-arg DOCKER_IMAGE=$(subst .$(TAG),,$@) \
--build-arg DOCKER_TAG=$(TAG) \
--build-arg IRODS_VERSION=4.3.0 \
--label org.opencontainers.image.title="iRODS 4.3.0 client development, Ubuntu 18.04" \
--label org.opencontainers.image.title="iRODS 4.3.1 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) \
--label org.opencontainers.image.vendor=npg.sanger.ac.uk \
--tag $(DOCKER_PREFIX)/ub-18.04-irods-clients-dev-4.3.0:latest \
--tag $(DOCKER_PREFIX)/ub-18.04-irods-clients-dev-4.3.0:$(TAG) --file $< ./irods_clients_dev
--tag $(DOCKER_PREFIX)/ub-22.04-irods-clients-dev-4.3.1:latest \
--tag $(DOCKER_PREFIX)/ub-22.04-irods-clients-dev-4.3.1:$(TAG) --file $< ./irods_clients_dev
touch $@

ub-22.04-irods-clients-dev-4.3.1.$(TAG): irods_clients_dev/ubuntu/22.04/Dockerfile
ub-22.04-irods-clients-dev-4.3.2.$(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=4.3.1 \
--build-arg IRODS_VERSION=4.3.2 \
--build-arg DOCKER_IMAGE=$(subst .$(TAG),,$@) \
--build-arg DOCKER_TAG=$(TAG) \
--label org.opencontainers.image.title="iRODS 4.3.1 client development, Ubuntu 22.04" \
--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) \
--label org.opencontainers.image.vendor=npg.sanger.ac.uk \
--tag $(DOCKER_PREFIX)/ub-22.04-irods-clients-dev-4.3.1:latest \
--tag $(DOCKER_PREFIX)/ub-22.04-irods-clients-dev-4.3.1:$(TAG) --file $< ./irods_clients_dev
--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-4.3.2.$(TAG): irods_clients_dev/ubuntu/22.04/Dockerfile
ub-22.04-irods-clients-dev-4.3.3.$(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 IRODS_VERSION=4.3.3 \
--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.title="iRODS 4.3.3 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) \
--label org.opencontainers.image.vendor=npg.sanger.ac.uk \
--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
--tag $(DOCKER_PREFIX)/ub-22.04-irods-clients-dev-4.3.3:latest \
--tag $(DOCKER_PREFIX)/ub-22.04-irods-clients-dev-4.3.3:$(TAG) --file $< ./irods_clients_dev
touch $@

ub-22.04-irods-clients-dev-4.3-nightly.$(TAG): irods_clients_dev/ubuntu/22.04/Dockerfile.nightly
Expand Down
6 changes: 6 additions & 0 deletions docker/irods/scripts/configure_irods.sh
Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,12 @@ case "$IRODS_VERSION" in
python3 /var/lib/irods/scripts/setup_irods.py < /opt/docker/irods/config/4.3.x.setup_irods.py.in
;;
4.3.2)
patch /var/lib/irods/scripts/irods/controller.py /opt/docker/irods/patches/patch_controller.diff
# 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
;;
4.3.3)
patch /var/lib/irods/scripts/irods/controller.py /opt/docker/irods/patches/patch_controller.diff
# 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
;;
Expand Down
8 changes: 5 additions & 3 deletions docker/irods/ubuntu/16.04/Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -4,14 +4,15 @@ FROM $BASE_IMAGE
# This default is the latest usable version
ARG IRODS_VERSION="4.2.7"

ENV DEBIAN_FRONTEND=noninteractive

WORKDIR /opt/docker/irods

COPY ./scripts/*.sh ./scripts/
COPY ./config/* ./config/
COPY ./patches/* ./patches/

RUN echo "debconf debconf/frontend select Noninteractive" | debconf-set-selections && \
apt-get update && \
RUN apt-get update && \
apt-get install -q -y --no-install-recommends \
apt-transport-https \
ca-certificates \
Expand All @@ -29,7 +30,8 @@ RUN echo "debconf debconf/frontend select Noninteractive" | debconf-set-selectio

ENV LANG=en_GB.UTF-8 \
LANGUAGE=en_GB \
LC_ALL=en_GB.UTF-8
LC_ALL=en_GB.UTF-8 \
TZ=/Etc/UTC

RUN curl -sSL https://packages.irods.org/irods-signing-key.asc | apt-key add - && \
echo "deb [arch=amd64] https://packages.irods.org/apt $(lsb_release -sc) main" | \
Expand Down
8 changes: 5 additions & 3 deletions docker/irods/ubuntu/18.04/Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -6,14 +6,15 @@ ARG IRODS_VERSION="4.3.1"
# This is the Debian package revision number
ARG IRODS_REVISION="1"

ENV DEBIAN_FRONTEND=noninteractive

WORKDIR /opt/docker/irods

COPY ./scripts/*.sh ./scripts/
COPY ./config/* ./config/
COPY ./patches/* ./patches/

RUN echo "debconf debconf/frontend select Noninteractive" | debconf-set-selections && \
apt-get update && \
RUN apt-get update && \
apt-get install -q -y --no-install-recommends \
apt-utils \
ca-certificates \
Expand All @@ -33,7 +34,8 @@ RUN echo "debconf debconf/frontend select Noninteractive" | debconf-set-selectio

ENV LANG=en_GB.UTF-8 \
LANGUAGE=en_GB \
LC_ALL=en_GB.UTF-8
LC_ALL=en_GB.UTF-8 \
TZ=/Etc/UTC

RUN curl -sSL https://packages.irods.org/irods-signing-key.asc | apt-key add - && \
echo "deb [arch=amd64] https://packages.irods.org/apt $(lsb_release -sc) main" | \
Expand Down
8 changes: 5 additions & 3 deletions docker/irods/ubuntu/22.04/Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -6,14 +6,15 @@ ARG IRODS_VERSION="4.3.1"
# This is the Debian package revision number
ARG IRODS_REVISION="0"

ENV DEBIAN_FRONTEND=noninteractive

WORKDIR /opt/docker/irods

COPY ./scripts/*.sh ./scripts/
COPY ./config/* ./config/
COPY ./patches/* ./patches/

RUN echo "debconf debconf/frontend select Noninteractive" | debconf-set-selections && \
apt-get update && \
RUN apt-get update && \
apt-get install -q -y --no-install-recommends \
apt-utils \
ca-certificates \
Expand All @@ -33,7 +34,8 @@ RUN echo "debconf debconf/frontend select Noninteractive" | debconf-set-selectio

ENV LANG=en_GB.UTF-8 \
LANGUAGE=en_GB \
LC_ALL=en_GB.UTF-8
LC_ALL=en_GB.UTF-8 \
TZ=/Etc/UTC

RUN curl -sSL https://packages.irods.org/irods-signing-key.asc | apt-key add - && \
echo "deb [arch=amd64] https://packages.irods.org/apt $(lsb_release -sc) main" | \
Expand Down
5 changes: 3 additions & 2 deletions docker/irods/ubuntu/22.04/Dockerfile.nightly
Original file line number Diff line number Diff line change
Expand Up @@ -3,14 +3,15 @@ FROM $BASE_IMAGE

ARG IRODS_VERSION="nightly"

ENV DEBIAN_FRONTEND=noninteractive

WORKDIR /opt/docker/irods

COPY ./scripts/*.sh ./scripts/
COPY ./config/* ./config/
COPY ./patches/* ./patches/

RUN echo "debconf debconf/frontend select Noninteractive" | debconf-set-selections && \
apt-get update && \
RUN apt-get update && \
apt-get install -q -y --no-install-recommends \
apt-utils \
ca-certificates \
Expand Down
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