update base image from 22.04 to 24.04; install more dependencies; support requester-pays; better makefile

Author: SHuang-Broad

docker/lr-gcloud-samtools/Dockerfile

@@ -2,11 +2,11 @@
 # then support both gsutil and gcloud CLIs
 
 ############### stage 0: build samtools and bcftools from source
-FROM ubuntu:20.04
+FROM ubuntu:24.04 AS builder
 
 ARG DEBIAN_FRONTEND=noninteractive
-ARG SAMTOOLS_VERSION=1.18
-ARG BCFTOOLS_VERSION=1.18
+ARG SAMTOOLS_VERSION=1.23
+ARG BCFTOOLS_VERSION=1.23
 RUN apt-get -qqy update --fix-missing && \
     apt-get -qqy dist-upgrade && \
     apt-get -qqy install --no-install-recommends \
@@ -27,14 +27,14 @@ RUN apt-get -qqy update --fix-missing && \
     tar xjf samtools-${SAMTOOLS_VERSION}.tar.bz2 && \
     cd samtools-${SAMTOOLS_VERSION} \
         && ./configure --without-curses --enable-libcurl --with-libdeflate \
-        && make -s all all-htslib \
+        && make -j 4 -s all all-htslib \
         && make install install-htslib && \
     cd - && rm -rf samtools-${SAMTOOLS_VERSION}* && \
     wget https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2 && \
     tar xjf bcftools-${BCFTOOLS_VERSION}.tar.bz2 && \
     cd bcftools-${BCFTOOLS_VERSION} \
         && ./configure --without-curses \
-        && make -s \
+        && make -j 4 -s \
         && make install && \
     cd - && rm -rf bcftools-${BCFTOOLS_VERSION}* && \
     apt-get -qqy purge autoconf automake bzip2 gcc make wget && \
@@ -49,21 +49,26 @@ RUN apt-get -qqy update --fix-missing && \
     bcftools --help
 
 ############### stage 1: other commonly used bioinformatics utilities
-FROM ubuntu:20.04
+FROM ubuntu:24.04
 
 ENV HOME=/root
 
 # Define default command.
 CMD ["bash"]
 
 # copy from previous stage the binaries from samtools build
-COPY --from=0 /usr/local/bin/* /usr/local/bin/
+COPY --from=builder /usr/local/bin/* /usr/local/bin/
+COPY --from=builder /usr/local/libexec/bcftools /usr/local/libexec/bcftools
 
 #### Basic utilities
 ARG DEBIAN_FRONTEND=noninteractive
 RUN apt-get -qqy update --fix-missing && \
     apt-get -qqy dist-upgrade && \
     apt-get -qqy install --no-install-recommends \
+                 libcurl4t64 \
+                 libdeflate0 \
+                 liblzma5 \
+                 libbz2-1.0 \
                  apt-transport-https \
                  ca-certificates \
                  gnupg \
@@ -74,6 +79,7 @@ RUN apt-get -qqy update --fix-missing && \
                  datamash \
                  gawk \
                  less \
+                 rename \
                  pigz \
                  tabix \
                  tree \
@@ -98,4 +104,4 @@ RUN apt-get -qqy update --fix-missing && \
     bcftools --version
 
 
-COPY re-auth.sh /opt/
+COPY re-auth.sh /opt/

docker/lr-gcloud-samtools/Makefile

@@ -1,11 +1,28 @@
-VERSION = 0.1.3
+VERSION = 0.1.23
 TAG1 = us.gcr.io/broad-dsp-lrma/lr-gcloud-samtools:$(VERSION)
 TAG2 = us.gcr.io/broad-dsp-lrma/lr-gcloud-samtools:latest
 
+ARCH := $(shell uname -m)
+BUILDER_NAME := lr-builder
+
+# Set platform flag only when needed
+ifeq ($(ARCH), arm64)
+    PLATFORM_FLAG := --platform linux/amd64
+else
+    PLATFORM_FLAG :=
+endif
+
+.PHONY: all build push
+
 all: build push
 
 build:
-	docker build -t $(TAG1) -t $(TAG2) .
+	@docker buildx inspect $(BUILDER_NAME) > /dev/null 2>&1 || \
+		docker buildx create --name $(BUILDER_NAME) --use
+	@docker buildx use $(BUILDER_NAME)
+	docker buildx build $(PLATFORM_FLAG) \
+		--load \
+		-t $(TAG1) -t $(TAG2) .
 
 push:
 	docker push $(TAG1)

docker/lr-gcloud-samtools/re-auth.sh

@@ -2,5 +2,5 @@
 
 set -eu
 
-export GCS_OAUTH_TOKEN=`gcloud auth application-default print-access-token`
-
+export GCS_OAUTH_TOKEN=$(gcloud auth application-default print-access-token)
+export GCS_REQUESTER_PAYS_PROJECT=$(gcloud config get-value project)