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pkg-scripts/cytoscape-3.9.1-0.build.sh
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| #! /bin/bash | |
| # https://cytoscape.org/download-platforms.html | |
| set -xe | |
| PKG=cytoscape | |
| VERSION=3.9.1 | |
| BUILD=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 | |
| . /pkg/openjdk-11.0.3.2-0/profile | |
| PATH=$PREFIX:\$PATH | |
| export JAVA_HOME=/pkg/openjdk-11.0.3.2-0 | |
| if [ -d $PREFIX/.compatlibs ]; then export LD_LIBRARY_PATH=$PREFIX/.compatlibs\${LD_LIBRARY_PATH:+:}\$LD_LIBRARY_PATH ; fi | |
| EOF | |
| . $PREFIX/profile | |
| BUILDDIR=$PREFIX/build | |
| mkdir -p $BUILDDIR | |
| # copy script to a known location (tools/build.sh may change behavior) | |
| cp $0 $BUILDDIR; ME="$BUILDDIR/$(basename $0)" | |
| cd $BUILDDIR | |
| # orig: https://github.com/cytoscape/cytoscape/releases/download/3.9.1/cytoscape-unix-3.9.1.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/e3b38288d8786a82c78eca5af523df2a/cytoscape-unix-3.9.1.tar.gz | |
| test -e cytoscape-unix-$VERSION.tar.gz || wget -nv $BEEHIVE | |
| test -d cytoscape-unix-$VERSION || tar -xf cytoscape-unix-$VERSION.tar.gz | |
| mv cytoscape-unix-$VERSION/* $PREFIX | |
| # intentionally fail if not empty | |
| rmdir cytoscape-unix-$VERSION | |
| cd $PREFIX | |
| mv cytoscape.sh cytoscape | |
| sed -ne '/^#Epatch:options/ s/^#Epatch:\S* // p' $ME | patch -p1 --verbose | |
| rm $ME | |
| exit | |
| #Epatch:options Original scripts have the $HOME/.cytoscape setting prepared, but | |
| #Epatch:options here we also need to differentiate beween hosts with different memory. | |
| #Epatch:options --- cytoscape-3.9.1-0/cytoscape 2022-01-21 22:05:35.000000000 +0100 | |
| #Epatch:options +++ cytoscape-3.9.1-0/cytoscape 2022-11-21 15:15:49.002432251 +0100 | |
| #Epatch:options @@ -56,2 +56,2 @@ | |
| #Epatch:options -#vm_options_path=$HOME/.cytoscape | |
| #Epatch:options -vm_options_path=$script_path | |
| #Epatch:options +vm_options_path=$HOME/.cytoscape | |
| #Epatch:options +hostname_short=${HOSTNAME%%.*} | |
| #Epatch:options @@ -60 +60 @@ | |
| #Epatch:options -if [ ! -e "$vm_options_path/Cytoscape.vmoptions" -a -x "$script_path/gen_vmoptions.sh" ]; then | |
| #Epatch:options +if [ ! -e "$vm_options_path/Cytoscape.vmoptions.$hostname_short" -a -x "$script_path/gen_vmoptions.sh" ]; then | |
| #Epatch:options @@ -65,2 +65,2 @@ | |
| #Epatch:options -if [ -r $vm_options_path/Cytoscape.vmoptions ]; then | |
| #Epatch:options - JAVA_OPTS=`cat $vm_options_path/Cytoscape.vmoptions` | |
| #Epatch:options +if [ -r $vm_options_path/Cytoscape.vmoptions.$hostname_short ]; then | |
| #Epatch:options + JAVA_OPTS=`cat $vm_options_path/Cytoscape.vmoptions.$hostname_short` | |
| #Epatch:options | |
| #Epatch:options --- cytoscape-3.9.1-0/gen_vmoptions.sh.dist 2022-01-21 22:05:34.000000000 +0100 | |
| #Epatch:options +++ cytoscape-3.9.1-0/gen_vmoptions.sh 2022-11-21 14:47:27.268970017 +0100 | |
| #Epatch:options @@ -1,2 +1,2 @@ | |
| #Epatch:options -#!/bin/sh | |
| #Epatch:options -# Generates the Cytoscape.vmoptions file | |
| #Epatch:options +#!/bin/bash | |
| #Epatch:options +# Generates the Cytoscape.vmoptions file (hostbased, since we are mariux) | |
| #Epatch:options @@ -6,2 +6,2 @@ | |
| #Epatch:options -#vm_options_path="$HOME/.cytoscape" | |
| #Epatch:options -vm_options_path=$script_path | |
| #Epatch:options +vm_options_path="$HOME/.cytoscape" | |
| #Epatch:options +hostname_short=${HOSTNAME%%.*} | |
| #Epatch:options @@ -50,3 +50,3 @@ | |
| #Epatch:options -echo "-Xms"${minmem}M> "$vm_options_path/Cytoscape.vmoptions" | |
| #Epatch:options -echo "-Xmx"${maxmem}M>> "$vm_options_path/Cytoscape.vmoptions" | |
| #Epatch:options -echo "-Xss5M">> "$vm_options_path/Cytoscape.vmoptions" | |
| #Epatch:options +echo "-Xms"${minmem}M> "$vm_options_path/Cytoscape.vmoptions.$hostname_short" | |
| #Epatch:options +echo "-Xmx"${maxmem}M>> "$vm_options_path/Cytoscape.vmoptions.$hostname_short" | |
| #Epatch:options +echo "-Xss5M">> "$vm_options_path/Cytoscape.vmoptions.$hostname_short" |