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nextflow: add version 23.04.1
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A tool similar to snakemake, was usually installed on per user
basis, here is the first try to provide a stable package.

More info:
 - https://www.nextflow.io/
 - https://www.nextflow.io/docs/latest/index.html
thomas committed May 5, 2023
1 parent 1ddf4f0 commit dcde233
Showing 1 changed file with 86 additions and 0 deletions.
86 changes: 86 additions & 0 deletions nextflow-23.04.1-0.build.sh
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#! /bin/bash

set -xe
umask 022

PKG=nextflow
VERSION=23.04.1
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

BUILDDIR=$PREFIX/build
mkdir -p $BUILDDIR

cd $BUILDDIR

source /pkg/openjdk-17.0.2.8-0/profile

# the '-all' file is a zip archive ...
# orig: https://github.com/nextflow-io/nextflow/releases/download/v23.04.1/nextflow-23.04.1-all
BEEHIVE=https://beehive.molgen.mpg.de/95c40ead6d16a7a0dc12fdf6c2bfe557/nextflow-23.04.1-all
test -e nextflow-$VERSION-all || wget -nv $BEEHIVE

# effect: this extracts to $HOME/.nextflow/capsule/apps/nextflow-all_23.04.1
bash nextflow-$VERSION-all info

# 'install' jars under $PREFIX/lib
cd $PREFIX
rm -fr bin lib
mkdir bin lib
mv $HOME/.nextflow/capsule/apps/nextflow-all_$VERSION lib

# create a straightforward launcher
cat <<- LAUNCHER > bin/nextflow
#! /bin/bash
NF_XTMPDIR=\${NF_XTMPDIR:-/scratch/local2/\$USER/nextflow_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

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