diff --git a/docker/Makefile b/docker/Makefile index 2ea8e1b..b5da367 100644 --- a/docker/Makefile +++ b/docker/Makefile @@ -190,8 +190,9 @@ ub-18.04-irods-clients-4.2.11.$(TAG): irods_clients/ubuntu/Dockerfile ub-18.04-b --build-arg DOCKER_TAG=$(TAG) \ --build-arg IRODS_VERSION=4.2.11 \ --build-arg BATON_VERSION=4.1.0 \ - --build-arg HTSLIB_VERSION=1.17 \ - --build-arg SAMTOOLS_VERSION=1.17 \ + --build-arg HTSLIB_VERSION=1.18 \ + --build-arg SAMTOOLS_VERSION=1.18 \ + --build-arg BCFTOOLS_VERSION=1.18 \ --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) \ @@ -210,8 +211,9 @@ ub-18.04-irods-clients-dev-4.2.11.$(TAG): irods_clients_dev/ubuntu/Dockerfile --build-arg DOCKER_TAG=$(TAG) \ --build-arg IRODS_VERSION=4.2.11 \ --build-arg BATON_VERSION=4.1.0 \ - --build-arg HTSLIB_VERSION=1.17 \ - --build-arg SAMTOOLS_VERSION=1.17 \ + --build-arg HTSLIB_VERSION=1.18 \ + --build-arg SAMTOOLS_VERSION=1.18 \ + --build-arg BCFTOOLS_VERSION=1.18 \ --label org.opencontainers.image.title="iRODS 4.2.11 client development, Ubuntu 18.04" \ --label org.opencontainers.image.source=$(git_url) \ --label org.opencontainers.image.revision=$(git_commit) \ @@ -231,8 +233,9 @@ ub-18.04-irods-clients-4.2.12.$(TAG): irods_clients/ubuntu/Dockerfile ub-18.04-b --build-arg DOCKER_TAG=$(TAG) \ --build-arg IRODS_VERSION=4.2.12 \ --build-arg BATON_VERSION=4.1.0 \ - --build-arg HTSLIB_VERSION=1.17 \ - --build-arg SAMTOOLS_VERSION=1.17 \ + --build-arg HTSLIB_VERSION=1.18 \ + --build-arg SAMTOOLS_VERSION=1.18 \ + --build-arg BCFTOOLS_VERSION=1.18 \ --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) \ diff --git a/docker/base/minideb/bullseye/Dockerfile b/docker/base/minideb/bullseye/Dockerfile index 38809ff..de2f46c 100644 --- a/docker/base/minideb/bullseye/Dockerfile +++ b/docker/base/minideb/bullseye/Dockerfile @@ -1,4 +1,4 @@ -FROM bitnami/minideb:bullseye-amd64 as installer +FROM docker.io/bitnami/minideb:bullseye-amd64 as installer ENV DEBIAN_FRONTEND=noninteractive \ GOSU_VERSION=1.16 @@ -21,7 +21,7 @@ RUN echo 'debconf debconf/frontend select Noninteractive' | debconf-set-selectio RUN GOSU_VERSION=$GOSU_VERSION /opt/docker/base/scripts/install_gosu.sh && \ chmod +x /opt/docker/base/scripts/docker-entrypoint.sh -FROM bitnami/minideb:bullseye-amd64 +FROM docker.io/bitnami/minideb:bullseye-amd64 RUN echo 'debconf debconf/frontend select Noninteractive' | debconf-set-selections && \ apt-get update && \ diff --git a/docker/irods_clients/manifest.json b/docker/irods_clients/manifest.json index f5c5739..96bbde9 100644 --- a/docker/irods_clients/manifest.json +++ b/docker/irods_clients/manifest.json @@ -1,6 +1,7 @@ { "package": "irods-clients", "executable": [ + "ace2sam", "baton-chmod", "baton-do", "baton-get", @@ -9,6 +10,14 @@ "baton-metaquery", "baton-put", "baton-specificquery", + "bcftools", + "bgzip", + "blast2sam.pl", + "bowtie2sam.pl", + "color-chrs.pl", + "export2sam.pl", + "gff2gff.py", + "guess-ploidy.py", "htsfile", "iadmin", "ibun", @@ -18,7 +27,6 @@ "iclienthints", "icp", "ienv", - "ienv", "ierror", "iexecmd", "iexit", @@ -27,8 +35,6 @@ "igroupadmin", "ihelp", "iinit", - "iinit", - "ils", "ils", "ilsresc", "imcoll", @@ -36,6 +42,7 @@ "imiscsvrinfo", "imkdir", "imv", + "interpolate_sam.pl", "ipasswd", "iphybun", "iphymv", @@ -66,6 +73,25 @@ "iuserinfo", "ixmsg", "izonereport", - "samtools" + "maq2sam-long", + "maq2sam-short", + "md5fa", + "md5sum-lite", + "novo2sam.pl", + "plot-ampliconstats", + "plot-bamstats", + "plot-roh.py", + "psl2sam.pl", + "run-roh.pl", + "sam2vcf.pl", + "samtools", + "samtools.pl", + "seq_cache_populate.pl", + "soap2sam.pl", + "tabix", + "vcfutils.pl", + "wgsim", + "wgsim_eval.pl", + "zoom2sam.pl" ] } diff --git a/docker/irods_clients/ubuntu/Dockerfile b/docker/irods_clients/ubuntu/Dockerfile index 7f6d0e5..028f394 100644 --- a/docker/irods_clients/ubuntu/Dockerfile +++ b/docker/irods_clients/ubuntu/Dockerfile @@ -6,8 +6,9 @@ FROM $BASE_IMAGE as installer # Other iRODS versions available on bionic are 4.3.0 ARG IRODS_VERSION="4.2.11" ARG BATON_VERSION="4.1.0" -ARG HTSLIB_VERSION="1.17" -ARG SAMTOOLS_VERSION="1.17" +ARG HTSLIB_VERSION="1.18" +ARG SAMTOOLS_VERSION="1.18" +ARG BCFTOOLS_VERSION="1.18" ARG HTSLIB_PLUGINS_VERSION="201712" COPY . /opt/docker/irods_clients @@ -87,6 +88,13 @@ RUN cd /tmp && \ ./configure --with-htslib=system --without-curses && \ make install +RUN cd /tmp && \ + curl -sSL -O "https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2" && \ + tar xfj bcftools-${BCFTOOLS_VERSION}.tar.bz2 && \ + cd bcftools-${BCFTOOLS_VERSION} && \ + ./configure --with-htslib=system --without-curses && \ + make install + RUN cd /tmp && \ git clone --depth 1 --branch ${HTSLIB_PLUGINS_VERSION} "https://github.com/samtools/htslib-plugins.git" && \ cd htslib-plugins && \ @@ -121,6 +129,7 @@ RUN curl -sSL https://packages.irods.org/irods-signing-key.asc | apt-key add - & tee /etc/apt/sources.list.d/renci-irods.list && \ apt-get update && \ apt-get install -q -y --no-install-recommends \ + gnuplot \ irods-icommands="${IRODS_VERSION}-1~$(lsb_release -sc)" \ irods-runtime="${IRODS_VERSION}-1~$(lsb_release -sc)" \ jq \ @@ -128,6 +137,7 @@ RUN curl -sSL https://packages.irods.org/irods-signing-key.asc | apt-key add - & libbz2-1.0 \ libcurl3 \ liblzma5 \ + perl \ zlib1g \ unattended-upgrades && \ unattended-upgrade -v && \ @@ -143,7 +153,6 @@ COPY --from=installer /usr/local /usr/local COPY --from=singularity ./scripts/* /usr/local/bin/ COPY --from=installer /opt/docker/irods_clients/manifest.json /usr/local/irods_clients/etc/manifest.json COPY --from=installer /opt/docker/irods_clients/scripts/docker-entrypoint.sh /usr/local/irods_clients/bin/docker-entrypoint.sh -COPY --from=installer /opt/docker/irods_clients/scripts/singularity-* /usr/local/bin/ # Configure the singularity-wrapper script ENV MANIFEST_PATH="/usr/local/irods_clients/etc/manifest.json"