Merge pull request #63 from dkj/samtools118

Samtools/bcftools 1.18 & [reduced] bonus controversy
wtsi-npg · Aug 8, 2023 · cf85a21 · cf85a21
2 parents da0609e + fc5c5be
commit cf85a21
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Showing 4 changed files with 53 additions and 15 deletions.
diff --git 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
@@ -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
@@ -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",
@@ -27,15 +35,14 @@
         "igroupadmin",
         "ihelp",
         "iinit",
-        "iinit",
-        "ils",
         "ils",
         "ilsresc",
         "imcoll",
         "imeta",
         "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
@@ -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 ${HTSLIB_PLUGINS_VERSION} "https://github.com/samtools/htslib-plugins.git" && \
     cd htslib-plugins && \
@@ -121,13 +129,15 @@ RUN curl -sSL https://packages.irods.org/irods-signing-key.asc | apt-key add - &
     tee /etc/apt/sources.list.d/renci-irods.list && \
     apt-get update && \ 
     apt-get install -q -y --no-install-recommends \
+    gnuplot \
     irods-icommands="${IRODS_VERSION}-1~$(lsb_release -sc)" \
     irods-runtime="${IRODS_VERSION}-1~$(lsb_release -sc)" \
     jq \
     libjansson4 \
     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"