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pkg-scripts/nextflow-22.10.0-0.build.sh
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| #! /bin/bash | |
| set -e | |
| umask 022 | |
| PKG=nextflow | |
| VERSION=22.10.0 | |
| BUILD=0 | |
| JDK=/pkg/openjdk-17.0.2.8-0 | |
| PREFIX=/pkg/$PKG-$VERSION-$BUILD | |
| if [ -n "$TESTING" ]; then PREFIX=/scratch/local2/$USER/$PKG-$VERSION-$BUILD ; fi | |
| mkdir -p $PREFIX | |
| cat >$PREFIX/profile <<-EOF | |
| PATH=$PREFIX/bin:\$PATH | |
| if [ -d $PREFIX/.compatlibs ]; then export LD_LIBRARY_PATH=$PREFIX/.compatlibs\${LD_LIBRARY_PATH:+:}\$LD_LIBRARY_PATH ; fi | |
| EOF | |
| . $PREFIX/profile | |
| BUILD_TMPDIR=/scratch/local2/$PKG-$VERSION-$BUILD-$USER.build.tmp | |
| test -d $BUILD_TMPDIR && rm -r $BUILD_TMPDIR | |
| export TMPDIR=$BUILD_TMPDIR | |
| export HOME=$BUILD_TMPDIR/home | |
| mkdir -p $HOME | |
| export NXF_HOME=$HOME/.nextflow.$VERSION | |
| BUILDDIR=$PREFIX/build | |
| mkdir -p $BUILDDIR | |
| cd $BUILDDIR | |
| source $JDK/profile | |
| # the '-all' file is a zip archive ... | |
| # orig: https://github.com/nextflow-io/nextflow/releases/download/v22.10.0/nextflow-22.10.0-all | |
| BEEHIVE=https://beehive.molgen.mpg.de/cc90e1fdc41eed849a15894f4e9a2b9f/nextflow-$VERSION-all | |
| test -e nextflow-$VERSION-all || wget -nv $BEEHIVE | |
| # effect: this extracts to $HOME/.nextflow/capsule/apps/nextflow-all_'version' | |
| bash nextflow-$VERSION-all info | |
| # 'install' jars under $PREFIX/lib | |
| cd $PREFIX | |
| rm -fr bin lib | |
| mkdir bin lib | |
| # get rid of '.lock', '.extracted' | |
| rm -v $HOME/.nextflow.$VERSION/capsule/apps/nextflow-all_$VERSION/.[a-z]* | |
| mv $HOME/.nextflow.$VERSION/capsule/apps/nextflow-all_$VERSION lib | |
| # create a straightforward launcher | |
| # Reflection, and migrating from Java-8 upwards: | |
| # [... use] --add-opens to open a package, which makes all its types and members accessible | |
| cat <<- LAUNCHER > bin/nextflow | |
| #! /usr/bin/bash | |
| if [ -z "\$NXF_HOME" ]; then | |
| export NXF_HOME=\$HOME/.nextflow.$VERSION | |
| fi | |
| NXF_PLUGINS_MODE=${NXF_PLUGINS_MODE:-prod} | |
| export NXF_PLUGINS_MODE | |
| NXF_PLUGINS_DIR=\${NXF_PLUGINS_DIR:-\$NXF_HOME/plugins} | |
| mkdir -vp "\$NXF_PLUGINS_DIR" | |
| export NXF_PLUGINS_DIR | |
| NF_XTMPDIR=\${NF_XTMPDIR:-/scratch/local2/\$USER/nextflow.${VERSION}_tmp} | |
| mkdir -vp "\$NF_XTMPDIR" | |
| exec $JDK/bin/java \\ | |
| --add-opens=java.base/java.lang=ALL-UNNAMED \\ | |
| --add-opens=java.base/java.io=ALL-UNNAMED \\ | |
| --add-opens=java.base/java.nio=ALL-UNNAMED \\ | |
| --add-opens=java.base/java.net=ALL-UNNAMED \\ | |
| --add-opens=java.base/java.util=ALL-UNNAMED \\ | |
| --add-opens=java.base/java.util.concurrent.locks=ALL-UNNAMED \\ | |
| --add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED \\ | |
| --add-opens=java.base/java.nio.file.spi=ALL-UNNAMED \\ | |
| --add-opens=java.base/sun.nio.ch=ALL-UNNAMED \\ | |
| --add-opens=java.base/sun.nio.fs=ALL-UNNAMED \\ | |
| --add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED \\ | |
| --add-opens=java.base/sun.net.www.protocol.https=ALL-UNNAMED \\ | |
| --add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED \\ | |
| --add-opens=java.base/sun.net.www.protocol.file=ALL-UNNAMED \\ | |
| --add-opens=java.base/jdk.internal.misc=ALL-UNNAMED \\ | |
| --add-opens=java.base/java.util.regex=ALL-UNNAMED \\ | |
| \\ | |
| -Djava.io.tmpdir="\$NF_XTMPDIR" \\ | |
| -Dfile.encoding=UTF-8 \\ | |
| -Djava.awt.headless=true \\ | |
| -Dcom.sun.security.enableAIAcaIssuers=true \\ | |
| -classpath '$PREFIX/lib/nextflow-all_$VERSION/*' \\ | |
| nextflow.cli.Launcher \\ | |
| "\${@+\$@}" | |
| LAUNCHER | |
| chmod -c +x bin/nextflow | |
| exit |