Add recipe for Cytoscape 3.7.1. (#14456)

recipes/cytoscape/LICENSE

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+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
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recipes/cytoscape/build.sh

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+#!/bin/bash
+
+outdir=${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM}
+envsubst '${PREFIX}:${PKG_NAME}:${PKG_VERSION}:${PKG_BUILDNUM}' < ${RECIPE_DIR}/response.varfile.template > response.varfile
+sh Cytoscape.sh -q -varfile response.varfile
+envsubst '${PREFIX}:${PKG_NAME}:${PKG_VERSION}:${PKG_BUILDNUM}' < ${RECIPE_DIR}/cytoscape.sh.template > $outdir/cytoscape.sh
+
+ln -s $outdir/Cytoscape ${PREFIX}/bin
+ln -s $outdir/cytoscape.sh ${PREFIX}/bin
+ln -s $outdir/gen_vmoptions.sh ${PREFIX}/bin

recipes/cytoscape/cytoscape.sh.template

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+#!/bin/bash
+#
+# Run cytoscape from a jar file
+# This script is a UNIX-only (i.e. Linux, Mac OS, etc.) version
+#-------------------------------------------------------------------------------
+
+# First, see if help (-h, --help) or version (-v, --version) command line arguments
+# are specified. If so, display help or the current version and exit.
+
+CYTOSCAPE_VERSION="Cytoscape version: 3.7.1"
+
+if [[ $# > 0 ]]; then
+	if [ $1 == "-h" -o $1 == "--help" ]; then
+		cat <<-EOF
+		
+	Cytoscape Command-line Arguments
+	================================
+	usage: cytoscape.{sh|bat} [OPTIONS]
+	 -h,--help             Print this message.
+	 -v,--version          Print the version number.
+	 -s,--session <file>   Load a cytoscape session (.cys) file.
+	 -N,--network <file>   Load a network file (any format).
+	 -P,--props <file>     Load cytoscape properties file (Java properties
+	                       format) or individual property: -P name=value.
+	 -V,--vizmap <file>    Load vizmap properties file (Cytoscape VizMap
+	                       format).
+	 -S,--script <file>    Execute commands from script file.
+	 -R,--rest <port>      Start a rest service.
+	 
+	EOF
+		exit 0
+	fi
+
+	if [ $1 == "-v" -o $1 == "--version" ]; then
+		echo $CYTOSCAPE_VERSION
+		exit 0
+	fi
+fi
+
+DEBUG_PORT=12345
+
+script_path="${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM}"
+
+export JAVA_DEBUG_OPTS="-Xdebug -Xnoagent -Djava.compiler=NONE -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=${DEBUG_PORT}"
+if [ `uname` = "Darwin" ]; then
+	CYTOSCAPE_MAC_OPTS="-Xdock:icon=$script_path/framework/cytoscape_logo_512.png -Xdock:name=Cytoscape"
+fi
+
+#vm_options_path=$HOME/.cytoscape
+vm_options_path=$script_path
+
+# Attempt to generate Cytoscape.vmoptions if it doesn't exist!
+if [ ! -e "$vm_options_path/Cytoscape.vmoptions"  -a  -x "$script_path/gen_vmoptions.sh" ]; then
+    "$script_path/gen_vmoptions.sh"
+fi
+
+export JAVA_OPTS=-Xms1550M\ -Xmx1550M
+if [ -r $vm_options_path/Cytoscape.vmoptions ]; then
+		JAVA_OPTS=`cat $vm_options_path/Cytoscape.vmoptions`
+else # Just use sensible defaults.
+    echo '*** Missing Cytoscape.vmoptions, falling back to using defaults!'
+		# Initialize MAX_MEM to something reasonable
+		JAVA_OPTS=-Xms1550M\ -Xmx1550M
+fi
+
+# The Cytoscape home directory contains the "framework" directory
+# and this script.
+CYTOSCAPE_HOME_REL=$script_path
+CYTOSCAPE_HOME_ABS=`cd "$CYTOSCAPE_HOME_REL"; pwd`
+
+export KARAF_OPTS=-Dcytoscape.home="$CYTOSCAPE_HOME_ABS"\ "$CYTOSCAPE_MAC_OPTS"
+
+export KARAF_DATA="${HOME}/CytoscapeConfiguration/3/karaf_data"
+mkdir -p "${KARAF_DATA}/tmp"
+
+$script_path/framework/bin/karaf "$@"

recipes/cytoscape/meta.yaml

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+{% set name = "cytoscape" %}
+{% set version = "3.7.1" %}
+{% set sha256 = "d1ad19c45a3bc6cfa6942a24eb599a5d935299948b9853145d75f698e3dd03d8" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  fn: Cytoscape.sh
+  url: https://github.com/cytoscape/cytoscape/releases/download/{{ version }}/Cytoscape_{{ version|replace(".","_") }}_unix.sh
+  sha256: {{ sha256 }}
+
+build:
+  number: 0
+  # skipping OSX for now due to installer bundling Java
+  skip: True # [osx]
+
+requirements:
+  build:
+    - gettext
+  host:
+    # Cytoscape requires Java 8 (9+ not supported)
+    - openjdk=8
+    - fontconfig
+    - freetype
+    - font-ttf-dejavu-sans-mono
+  run:
+    - openjdk=8
+    - xorg-libxtst
+    - fontconfig
+    - freetype
+    - font-ttf-dejavu-sans-mono
+
+test:
+  commands:
+    - "cytoscape.sh -v"
+
+about:
+  home: https://cytoscape.org
+  license: LGPL
+  license_family: GPL
+  license_file: '{{ environ["RECIPE_DIR"] }}/LICENSE'
+  summary: 'Cytoscape: an open source platform for network analysis and visualization.'
+  dev_url: https://github.com/cytoscape/cytoscape
+
+extra:
+  identifiers:
+    - biotools:cytoscape
+    - doi:10.1101/gr.1239303
+  skip-lints:
+    - should_not_use_fn

recipes/cytoscape/response.varfile.template

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+# install4j response file for Cytoscape 3.7.1
+ShareStatistics$Boolean=false
+sys.adminRights$Boolean=false
+sys.component.235$Boolean=true
+sys.installationDir=${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM}
+sys.languageId=en