# HG changeset patch
# User saskia-hiltemann
# Date 1412084834 14400
# Node ID e8755431a0cd8911bf27da9cb39d24c43980f447
# Parent  440f4aa3db97edda4e888615904dc8c62b2eeda9
fixed missing dependencies

diff -r 440f4aa3db97 -r e8755431a0cd README.md
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Tue Sep 30 09:47:14 2014 -0400
@@ -0,0 +1,24 @@
+iReport
+=======
+
+iReport Galaxy tool - HTML reporting in Galaxy
+
+install to your Galaxy via the main tool shed: http://toolshed.g2.bx.psu.edu/
+
+direct repository link:  http://saskia-hiltemann@toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/ireport
+
+email: s.hiltemann@erasmusmc.nl
+
+
+
+
+Planned changes
+---------------
+- ~~option to download iReport webpage~~
+- more pluggable code to add content item types etc.
+- markdown instead of plain text/html in text fields.
+- multiple columns in table converted to weblinks.
+- table colums link to archive files in history
+- ..
+- ..suggestions anyone?
+
diff -r 440f4aa3db97 -r e8755431a0cd iReport.sh
--- a/iReport.sh	Wed Jul 30 07:03:43 2014 -0400
+++ b/iReport.sh	Tue Sep 30 09:47:14 2014 -0400
@@ -1,5 +1,5 @@
 #!/bin/bash
-repositorypath="/mnt/galaxyTools/shed_tools/toolshed.nbic.nl/repos/saskia-hiltemann/ireport/71dc132e9bb2/ireport"  # TODO: dependency
+#repositorypath="/mnt/galaxyTools/shed_tools/toolshed.nbic.nl/repos/saskia-hiltemann/ireport/71dc132e9bb2/ireport"  # TODO: dependency
 source "${repositorypath}/createHTML.sh"
 
 echo "allparams: $@"
@@ -15,8 +15,8 @@
 while [ $# -gt 0 ]
 do
     case "$1" in
-       	--toolpath)      		repositorypath=$2;shift;;  
-		--galaxypath)			galaxypath=$2;shift;; 
+       	--toolpath)				repositorypath=$2;shift;;
+		--galaxypath)			galaxypath=$2;shift;;
 		--minwidth)				minwidth=$2;shift;; 
 		--tab)					tabs+=",$2";shift;;
 		--item)					items+=",$2";shift;;
diff -r 440f4aa3db97 -r e8755431a0cd iReport.xml
--- a/iReport.xml	Wed Jul 30 07:03:43 2014 -0400
+++ b/iReport.xml	Tue Sep 30 09:47:14 2014 -0400
@@ -1,10 +1,13 @@
 <tool id="iReport" name="iReport" version="1">
  	<description> create an HTML report </description>
 	
-
+	<requirements>
+		<requirement type="set_environment">REPOSITORY_PATH</requirement>
+	</requirements>
   	<command interpreter="bash"> 
 		
   		iReport.sh 
+			--toolpath \$REPOSITORY_PATH
 			--galaxypath ${report.files_path}
 			--htmlout ${report}
 			--minwidth ${minwidth}
diff -r 440f4aa3db97 -r e8755431a0cd tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Sep 30 09:47:14 2014 -0400
@@ -0,0 +1,7 @@
+<?xml version="1.0"?>
+<tool_dependency>
+	<set_environment version="1.0">
+        <environment_variable name="REPOSITORY_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>               
+    </set_environment>
+</tool_dependency>
+