Merge pull request #3 from NCI-GDC/update_template

Update template

.cruft.json

@@ -1,12 +1,12 @@
 {
     "template": "[email protected]:NCI-GDC/bio-software-template.git",
-    "commit": "edc121c807074808a30cbf77e29d89cb1320f16a",
+    "commit": "7a4a06c3072e31fe76e22beacb12991004410dba",
     "context": {
       "cookiecutter": {
         "repository_name": "biobambam-docker",
-        "software_name": "biobambam",
-        "software_version": "1.0.0",
-        "commit": "edc121c807074808a30cbf77e29d89cb1320f16a",
+        "software_name": "biobambam2",
+        "software_version": "2.0.0",
+        "commit": "7a4a06c3072e31fe76e22beacb12991004410dba",
         "_template": "[email protected]:NCI-GDC/bio-software-template.git"
       }
     },

.gitlab-ci.yml

@@ -9,10 +9,13 @@ include:
     file:
       - templates/global/full.yaml
 
+variables:
+  DOCKER_VERSION: 27.4.0
+
 build_dockers:
   stage: build
   services:
-    - docker:20.10.16-dind
+    - docker:${DOCKER_VERSION}-dind
   tags:
     - dind
   before_script:

.pre-commit-config.yaml

@@ -1,14 +1,14 @@
 default_stages: [commit, push]
 
 repos:
-  - repo: git@github.com:Yelp/detect-secrets
-    rev: v1.2.0
+  - repo: https://github.com/Yelp/detect-secrets
+    rev: v1.4.0
     hooks:
       - id: detect-secrets
         args: ["--baseline", ".secrets.baseline"]
         exclude: ^(\.cruft\.json)$
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.1.0
+    rev: v4.2.0
     hooks:
       - id: check-yaml
       - id: check-toml

2.0.95/justfile

@@ -1,15 +1,19 @@
-SOFTWARE := "biobambam"
-DOCKERFILE := "./Dockerfile"
+SOFTWARE := "biobambam2"
+DOCKERFILE := "../Dockerfile.multi"
 BASE_CONTAINER_REGISTRY := env_var_or_default("BASE_CONTAINER_REGISTRY", "docker.osdc.io")
 
-VERSION := `basename $(pwd)`
+VERSION := "2.0.95-release-20190320141403"
 
 emit-dockerfile:
     @echo {{DOCKERFILE}}
 
+emit-version:
+  @echo {{VERSION}}
+
 build-docker:
   docker buildx build --compress --progress plain \
   -t "{{SOFTWARE}}-{{VERSION}}" \
   -f {{DOCKERFILE}} \
   . \
+  --build-arg VERSION="{{VERSION}}" \
   --build-arg REGISTRY="{{BASE_CONTAINER_REGISTRY}}"

Dockerfile.multi

@@ -1,77 +1,65 @@
 ARG REPOSITORY=docker.osdc.io
-ARG BUILDER_TAG=2.2.0
-FROM ${REPOSITORY}/ncigdc/base-u22.04-builder:${BUILDER_TAG} AS builder
+ARG BUILDER_TAG=3.1.0
 
+FROM scratch AS src
+
+ENV LIBMAUS_VERSION=2.0.610-release-20190328154814
+ARG VERSION
+ENV BIOBAMBAM_VERSION=${VERSION}
+
+ADD https://gitlab.com/german.tischler/libmaus2/-/archive/$LIBMAUS_VERSION/libmaus2-$LIBMAUS_VERSION.tar.gz /libmaus2.tar.gz
+ADD https://gitlab.com/german.tischler/biobambam2/-/archive/$BIOBAMBAM_VERSION/biobambam2-$BIOBAMBAM_VERSION.tar.gz /biobambam2.tar.gz
+
+FROM ${REPOSITORY}/ncigdc/amzn2023-builder:${BUILDER_TAG} AS builder
+
+ENV LIBMAUS_VERSION=2.0.610-release-20190328154814
 ARG VERSION
+ENV BIOBAMBAM_VERSION=${VERSION}
+
+RUN --mount=from=src,target=/src <<EOF
+mkdir -p /libmaus2
+tar -oxzf /src/libmaus2.tar.gz -C /libmaus2
+EOF
+
+RUN --mount=from=src,target=/src <<EOF
+mkdir -p /biobambam2
+tar -oxzf /src/biobambam2.tar.gz -C /biobambam2
+EOF
+
+RUN dnf install -y \
+	autoconf \
+	g++ \
+	libtool \
+	zlib-devel \
+	boost-devel \
+    automake
+
+ENV INSTALLDIR=/biobambam
+
+RUN mkdir -p ${INSTALLDIR}
+
+WORKDIR /libmaus2/libmaus2-$LIBMAUS_VERSION
+
+RUN <<EOF
+JOBS=$(cat /proc/cpuinfo | egrep "^processor" | wc -l)
+libtoolize
+aclocal
+autoreconf -i -f
+./configure --prefix=${INSTALLDIR}
+make -j ${JOBS}
+make -j ${JOBS} install
+EOF
+
+WORKDIR /biobambam2/biobambam2-$BIOBAMBAM_VERSION
+
+RUN <<EOF
+JOBS=$(cat /proc/cpuinfo | egrep "^processor" | wc -l)
+autoreconf -i -f
+LDFLAGS="-Wl,-rpath=$INSTALLDIR/lib -Wl,-z -Wl,origin" ./configure --with-libmaus2=${INSTALLDIR} --prefix=${INSTALLDIR}
+make -j ${JOBS}
+make -j ${JOBS} install
+EOF
+
+ENV PATH=/biobambam/bin:$PATH
 
-ENV URL=https://path/to/file/$VERSION/software-$VERSION.tar.gz
-    && curl --silent https://gitlab.com/german.tischler/libmaus2/repository/archive.tar.gz\?ref\=2.0.610-release-20190328154814 -o libmaus2.tar.gz \
-    && curl --silent https://gitlab.com/german.tischler/biobambam2/repository/archive.tar.gz\?ref\=2.0.95-release-20190320141403 -o biobambam2.tar.gz \
-
-RUN apt-get update \
-	&& apt-get install -y \
-		build-essential \
-	&& apt-get clean \
-	&& rm -rf /var/lib/apt/lists/*
-
-# Example download and compile step
-RUN wget $URL \
-	&& tar xf software-${VERSION}.tar.gz \
-	&& cd software-${VERSION} \
-	&& make \
-	&& mv bin/* /usr/local/bin \
-	&& cd .. \
-	&& rm -rf software-${VERSION}
-
-# For a multi-stage build
-
-FROM ${REPOSITORY}/ncigdc/base-u22.04:${BUILDER_TAG}
-
-COPY --from=builder /usr/local/* /usr/local/
-FROM ubuntu:disco-20190310
-
-MAINTAINER Jeremiah H. Savage <[email protected]>
-
-ENV LD_LIBRARY_PATH /usr/local/lib
-
-RUN apt-get update \
-    && apt-get install -y \
-        autoconf \
-        curl \
-        g++ \
-        libtool \
-        pkg-config \
-        zlib1g-dev \
-    && apt-get clean \
-    && rm -rf /usr/local/* \
-
-    && libmaus2files=$(tar -axvf libmaus2.tar.gz) \
-    && libmaus2dir=$(echo ${libmaus2files} | cut -f1 -d" ") \
-    && cd ${libmaus2dir} \
-    && libtoolize \
-    && aclocal \
-    && autoreconf -i -f \
-    && ./configure \
-    && make -j4 \
-    && make install \
-    && cd ../ \
-    && rm -rf ${libmaus2dir} libmaus2.tar.gz \
-    && biobambam2files=$(tar -axvf biobambam2.tar.gz) \
-    && biobambam2dir=$(echo ${biobambam2files} | cut -f1 -d" ") \
-    && cd ${biobambam2dir} \
-    && export LIBMAUSPREFIX=/usr/local \
-    && autoreconf -i -f \
-    && ./configure --with-libmaus2=${LIBMAUSPREFIX} \
-    && make -j4 \
-    && make install \
-    && cd ../ \
-    && rm -rf ${biobambam2dir} biobambam2.tar.gz \
-    && apt-get remove --purge -y \
-        autoconf \
-        curl \
-        g++ \
-        libtool \
-        pkg-config \
-        zlib1g-dev \
-    && apt-get autoremove -y \
-    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+ENTRYPOINT ["/usr/bin/dumb-init", "--"]