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executable file 102 lines (81 sloc) 3.13 KB
#! /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