[ci skip] Merge PR 19551

Merge PR #19551, commits were: 
 * luciphor2: replace - in version by _
 * luciphor2: initial commit

based on the opsin 2.4.0 recipe

recipes/luciphor2/build.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+set -eu -o pipefail
+
+outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM
+mkdir -p $outdir
+mkdir -p $PREFIX/bin
+cp luciphor*jar $outdir/luciphor2.jar
+cp $RECIPE_DIR/luciphor2.sh $outdir/luciphor2
+ln -s $outdir/luciphor2 $PREFIX/bin
+chmod 0755 "$outdir/luciphor2"

recipes/luciphor2/luciphor2.sh

@@ -0,0 +1,56 @@
+#!/bin/bash
+# Wraps opsin.jar
+set -o pipefail
+
+# Find original directory of bash script, resovling symlinks
+# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128
+SOURCE="${BASH_SOURCE[0]}"
+while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
+    DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+    SOURCE="$(readlink "$SOURCE")"
+    [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
+done
+DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+
+JAR_DIR=$DIR
+java=java
+if [ -e "$JAVA_HOME/bin/java" ]
+then
+java="$JAVA_HOME/bin/java"
+fi
+
+# extract memory and system property Java arguments from the list of provided arguments
+# http://java.dzone.com/articles/better-java-shell-script
+default_jvm_mem_opts="-Xms512m -Xmx1g"
+jvm_mem_opts=""
+jvm_prop_opts=""
+pass_args=""
+for arg in "$@"; do
+    case $arg in
+        '-D'*)
+            jvm_prop_opts="$jvm_prop_opts $arg"
+            ;;
+        '-XX'*)
+            jvm_prop_opts="$jvm_prop_opts $arg"
+            ;;
+         '-Xm'*)
+            jvm_mem_opts="$jvm_mem_opts $arg"
+            ;;
+         *)
+            pass_args="$pass_args $arg"
+            ;;
+    esac
+done
+
+if [ "$jvm_mem_opts" == "" ] && [ -z ${_JAVA_OPTIONS+x} ]; then
+    jvm_mem_opts="$default_jvm_mem_opts"
+fi
+
+pass_arr=($pass_args)
+if [[ ${pass_arr[0]} == org* ]]
+then
+    eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/luciphor2.jar" $pass_args
+else
+    eval "$java" $jvm_mem_opts $jvm_prop_opts -jar "$JAR_DIR/luciphor2.jar" $pass_args
+fi
+exit

recipes/luciphor2/meta.yaml

@@ -0,0 +1,37 @@
+{% set name = "luciphor2" %}
+{% set version = "2018-06-28" %}
+{% set sha256 = "79adf33ff629ce80f0010ead773e2cd5e855304d0685625f4921a4ba72990435" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version|replace("-", "_") }}
+
+source:
+  url: https://depot.galaxyproject.org/software/luciphor2/luciphor2_{{ version }}_all_all.jar
+  sha256: {{ sha256 }}
+
+build:
+  noarch: generic
+  number: 0
+
+requirements:
+  run:
+    - openjdk  >=6
+
+test:
+  commands:
+    - luciphor2
+
+about:
+  home: http://luciphor2.sourceforge.net/
+  license: Apache-2.0
+  summary: Luciphor2 performs PTM-site localization on MS/MS data
+
+extra:
+  notes: |
+    Adds a wrapper shell script "luciphor2".
+    This shell wrapper is called "luciphor2" and is on $PATH by default. By default
+    "-Xms512m -Xmx1g" is set in the wrapper. If you want to overwrite it you can
+    specify these values directly after your binaries. If you have _JAVA_OPTIONS
+    set globally this will take precedence.
+    For example run with "luciphor -Xms512m -Xmx1g"