Merge pull request #136 from kjsanger/feature/samtools-1.22

Update samtools/htslib to 1.22.1 and make these defaults

Author: kjsanger

docker/Makefile

@@ -13,9 +13,9 @@ DOCKER_PREFIX?=$(DOCKER_REGISTRY)/$(DOCKER_USER)
 DOCKER_ARGS ?= --platform linux/amd64 --progress=plain --rm
 
 BATON_VERSION=6.0.0
-HTSLIB_VERSION=1.20
-SAMTOOLS_VERSION=1.20
-BCFTOOLS_VERSION=1.20
+HTSLIB_VERSION=1.22.1
+SAMTOOLS_VERSION=1.22.1
+BCFTOOLS_VERSION=1.22
 
 .PHONY: clean push
 

docker/irods_clients/ubuntu/16.04/Dockerfile

@@ -61,7 +61,7 @@ RUN apt-get update && \
 ENV CPPFLAGS="-I/usr/include/irods"
 ENV CPU_COUNT=4
 
-ARG BATON_VERSION="4.3.2"
+ARG BATON_VERSION="6.0.0"
 
 RUN cd /tmp && \
     curl -sSL -O "https://github.com/wtsi-npg/baton/releases/download/${BATON_VERSION}/baton-${BATON_VERSION}.tar.gz" && \
@@ -70,7 +70,7 @@ RUN cd /tmp && \
     ./configure && \
     make -j ${CPU_COUNT} install
 
-ARG HTSLIB_VERSION="1.18"
+ARG HTSLIB_VERSION="1.22.1"
 
 RUN cd /tmp && \
     curl -sSL -O "https://github.com/samtools/htslib/releases/download/${HTSLIB_VERSION}/htslib-${HTSLIB_VERSION}.tar.bz2" && \
@@ -80,7 +80,7 @@ RUN cd /tmp && \
     make -j ${CPU_COUNT} install && \
     ldconfig
 
-ARG SAMTOOLS_VERSION="1.18"
+ARG SAMTOOLS_VERSION="1.22.1"
 
 RUN cd /tmp && \
     curl -sSL -O "https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2" && \
@@ -89,7 +89,7 @@ RUN cd /tmp && \
     ./configure --with-htslib=system --without-curses && \
     make -j ${CPU_COUNT} install
 
-ARG BCFTOOLS_VERSION="1.18"
+ARG BCFTOOLS_VERSION="1.22"
 
 RUN cd /tmp && \
     curl -sSL -O "https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2" && \

docker/irods_clients/ubuntu/18.04/Dockerfile

@@ -63,7 +63,7 @@ RUN apt-get update && \
 ENV CPPFLAGS="-I/usr/include/irods"
 ENV CPU_COUNT=4
 
-ARG BATON_VERSION="4.3.2"
+ARG BATON_VERSION="6.0.0"
 
 RUN cd /tmp && \
     curl -sSL -O "https://github.com/wtsi-npg/baton/releases/download/${BATON_VERSION}/baton-${BATON_VERSION}.tar.gz" && \
@@ -72,7 +72,7 @@ RUN cd /tmp && \
     ./configure && \
     make -j ${CPU_COUNT} install
 
-ARG HTSLIB_VERSION="1.18"
+ARG HTSLIB_VERSION="1.22.1"
 
 RUN cd /tmp && \
     curl -sSL -O "https://github.com/samtools/htslib/releases/download/${HTSLIB_VERSION}/htslib-${HTSLIB_VERSION}.tar.bz2" && \
@@ -82,7 +82,7 @@ RUN cd /tmp && \
     make -j ${CPU_COUNT} install && \
     ldconfig
 
-ARG SAMTOOLS_VERSION="1.18"
+ARG SAMTOOLS_VERSION="1.22.1"
 
 RUN cd /tmp && \
     curl -sSL -O "https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2" && \
@@ -91,7 +91,7 @@ RUN cd /tmp && \
     ./configure --with-htslib=system --without-curses && \
     make -j ${CPU_COUNT} install
 
-ARG BCFTOOLS_VERSION="1.18"
+ARG BCFTOOLS_VERSION="1.22"
 
 RUN cd /tmp && \
     curl -sSL -O "https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2" && \

docker/irods_clients/ubuntu/18.04/README.md

@@ -20,10 +20,10 @@ The Dockerfile supports these build arguments:
 - DOCKER_IMAGE (no default, must be supplied)
 - DOCKER_TAG (no default, must be supplied)
 - IRODS_VERSION (defaults to the latest usable iRODS version, currently "4.3.1")
-- BATON_VERSION (defaults to "4.2.1")
-- HTSLIB_VERSION (defaults to "1.18")
-- SAMTOOLS_VERSION (defaults to "1.18")
-- BCFTOOLS_VERSION (defaults to "1.18")
+- BATON_VERSION (defaults to "6.0.0")
+- HTSLIB_VERSION (defaults to "1.22.1")
+- SAMTOOLS_VERSION (defaults to "1.22.1")
+- BCFTOOLS_VERSION (defaults to "1.22")
 - HTSLIB_PLUGINS_VERSION (defaults to "201712")
 
 The Dockerfile creates a local user `appuser` with a `UID` of `1000` whose

docker/irods_clients/ubuntu/22.04/Dockerfile

@@ -56,7 +56,7 @@ RUN apt-get update && \
 ENV CPPFLAGS="-I/usr/include/irods"
 ENV CPU_COUNT=4
 
-ARG BATON_VERSION="4.3.2"
+ARG BATON_VERSION="6.0.0"
 
 RUN cd /tmp && \
     curl -sSL -O "https://github.com/wtsi-npg/baton/releases/download/${BATON_VERSION}/baton-${BATON_VERSION}.tar.gz" && \
@@ -65,7 +65,7 @@ RUN cd /tmp && \
     ./configure && \
     make -j ${CPU_COUNT} install
 
-ARG HTSLIB_VERSION="1.18"
+ARG HTSLIB_VERSION="1.22.1"
 
 RUN cd /tmp && \
     curl -sSL -O "https://github.com/samtools/htslib/releases/download/${HTSLIB_VERSION}/htslib-${HTSLIB_VERSION}.tar.bz2" && \
@@ -75,7 +75,7 @@ RUN cd /tmp && \
     make -j ${CPU_COUNT} install && \
     ldconfig
 
-ARG SAMTOOLS_VERSION="1.18"
+ARG SAMTOOLS_VERSION="1.22.1"
 
 RUN cd /tmp && \
     curl -sSL -O "https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2" && \
@@ -84,7 +84,7 @@ RUN cd /tmp && \
     ./configure --with-htslib=system --without-curses && \
     make -j ${CPU_COUNT} install
 
-ARG BCFTOOLS_VERSION="1.18"
+ARG BCFTOOLS_VERSION="1.22"
 
 RUN cd /tmp && \
     curl -sSL -O "https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2" && \

docker/irods_clients/ubuntu/22.04/README.md

@@ -20,10 +20,10 @@ The Dockerfile supports these build arguments:
 - DOCKER_IMAGE (no default, must be supplied)
 - DOCKER_TAG (no default, must be supplied)
 - IRODS_VERSION (defaults to the latest usable iRODS version, currently "4.3.1")
-- BATON_VERSION (defaults to "4.2.1")
-- HTSLIB_VERSION (defaults to "1.18")
-- SAMTOOLS_VERSION (defaults to "1.18")
-- BCFTOOLS_VERSION (defaults to "1.18")
+- BATON_VERSION (defaults to "6.00")
+- HTSLIB_VERSION (defaults to "1.22.1")
+- SAMTOOLS_VERSION (defaults to "1.22.1")
+- BCFTOOLS_VERSION (defaults to "1.22")
 - HTSLIB_PLUGINS_VERSION (defaults to "201712")
 
 The Dockerfile creates a local user `appuser` with a `UID` of `1000` whose