From a254e891101fcdf160ef37605738361f0b42f667 Mon Sep 17 00:00:00 2001
From: thomas <kreitler@molgen.mpg.de>
Date: Thu, 6 Mar 2025 12:01:08 +0100
Subject: [PATCH] nextflow: add version 24.10.5

Setup process seems to be simplified compared to v.23 .
Also we can now just use the default java runtime.
---
 nextflow-24.10.5-0.build.sh | 65 +++++++++++++++++++++++++++++++++++++
 1 file changed, 65 insertions(+)
 create mode 100755 nextflow-24.10.5-0.build.sh

diff --git a/nextflow-24.10.5-0.build.sh b/nextflow-24.10.5-0.build.sh
new file mode 100755
index 0000000..2f4f76e
--- /dev/null
+++ b/nextflow-24.10.5-0.build.sh
@@ -0,0 +1,65 @@
+#! /bin/bash
+
+set -eu
+umask 022
+
+PKG=nextflow
+VERSION=24.10.5
+BUILD=0
+
+PREFIX=/pkg/$PKG-$VERSION-$BUILD
+
+TESTING=${TESTING:-}
+if [ -n "$TESTING" ]; then PREFIX=/scratch/local2/$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
+
+cd $PREFIX
+rm -fr bin
+mkdir bin
+cd bin
+
+# the '-dist' file is a zip/jar with a 511 line bash stub ...
+# orig: https://github.com/nextflow-io/nextflow/releases/download/v24.10.5/nextflow-24.10.5-dist
+BEEHIVE=https://beehive.molgen.mpg.de/9255e04a1787ccd8bcbe6db4e456dc7e/nextflow-24.10.5-dist
+test -e nextflow-$VERSION-dist || wget -nv $BEEHIVE
+
+# ... and do not always check for updates, please
+sed -i -e '509 s/check_latest/# skip_check/' nextflow-$VERSION-dist
+
+chmod -c 0755 nextflow-$VERSION-dist
+
+cat <<- LAUNCHER > nextflow
+	#! /usr/bin/bash
+
+	NXF_PLUGINS_MODE=\${NXF_PLUGINS_MODE:-prod}
+	export NXF_PLUGINS_MODE
+
+	NXF_PLUGINS_DIR=\${NXF_PLUGINS_DIR:-\$HOME/.nextflow/plugins}
+	mkdir -vp "\$NXF_PLUGINS_DIR"
+	export NXF_PLUGINS_DIR
+
+	NXF_TEMP=\${NXF_TEMP:-/scratch/local2/\$USER/nextflow_tmp}
+	mkdir -vp "\$NXF_TEMP"
+	export NXF_TEMP
+
+	exec \\
+	  nextflow-$VERSION-dist \\
+	  "\${@+\$@}"
+
+LAUNCHER
+
+chmod -c +x nextflow
+
+exit