Mercurial > repos > iuc > package_peptideshaker_0_20_1

changeset 0:c661fad47f03 draft default tip

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author iuc
date Fri, 11 Apr 2014 16:30:10 -0400
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files tool_dependencies.xml
diffstat 1 files changed, 61 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Apr 11 16:30:10 2014 -0400
@@ -0,0 +1,61 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="peptide_shaker" version="0.20.1">
+    <install version="1.0">
+        <actions>
+            <action type="download_by_url">http://peptide-shaker.googlecode.com/files/PeptideShaker-0.20.1.zip</action>
+            <action type="shell_command">chmod -R o+w resources</action>
+            <action type="shell_command">wget https://gist.github.com/jmchilton/5002161/raw/f1fe76d6e6eed99a768ed0b9f41c2d0a6a4b24b7/PeptideShaker</action>
+<!--
+#!/bin/bash
+
+SOURCE="${BASH_SOURCE[0]}"
+app_dir="$( dirname "$SOURCE" )"
+while [ -h "$SOURCE" ]
+do
+  SOURCE="$(readlink "$SOURCE")"
+  [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE"
+  app_dir="$( cd -P "$( dirname "$SOURCE"  )" && pwd )"
+done
+app_dir="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+
+jar=`find "$app_dir" -iname "PeptideShaker*jar"`
+cd "$app_dir"
+java -jar "$jar" "$@"
+-->
+        <action type="shell_command">wget https://gist.github.com/jmchilton/5002161/raw/8a17d5fb589984365284e55a98a455c2b47da54f/PeptideShakerCLI</action>
+<!--
+#!/bin/bash
+
+SOURCE="${BASH_SOURCE[0]}"
+app_dir="$( dirname "$SOURCE" )"
+while [ -h "$SOURCE" ]
+do
+  SOURCE="$(readlink "$SOURCE")"
+  [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE"
+  app_dir="$( cd -P "$( dirname "$SOURCE"  )" && pwd )"
+done
+app_dir="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+
+jar=`find "$app_dir" -iname "PeptideShaker*jar"`
+cd "$app_dir"
+java -cp "$jar" eu.isas.peptideshaker.cmd.PeptideShakerCLI  "$@"
+-->
+            <action type="shell_command">chmod +x PeptideShaker</action>
+            <action type="shell_command">chmod +x PeptideShakerCLI</action>
+            <action type="move_directory_files">
+                <source_directory>.</source_directory>
+                <destination_directory>$INSTALL_DIR/</destination_directory>
+            </action>
+            <action type="set_environment">
+                <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                <environment_variable name="PEPTIDESHAKER_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable>
+                <environment_variable name="PEPTIDESHAKER_JAR_PATH" action="set_to">$INSTALL_DIR/PeptideShaker-0.20.1.jar</environment_variable>
+            </action>
+        </actions>
+    </install>
+    <readme>
+        Install Galaxy package application for PeptideShaker 0.20.1.
+    </readme>
+  </package>
+</tool_dependency>