-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
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
Showing
1 changed file
with
86 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,86 @@ | ||
#! /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 |