# HG changeset patch
# User stef
# Date 1415268557 18000
# Node ID 0feb7fa372458a4be90b6d5bdd0e92144e82b430
# Parent  4db025c51b6ee1675d35636029fab8d815bb5022
Uploaded

diff -r 4db025c51b6e -r 0feb7fa37245 QDNAseq.R
--- a/QDNAseq.R	Fri Oct 24 07:06:55 2014 -0400
+++ b/QDNAseq.R	Thu Nov 06 05:09:17 2014 -0500
@@ -135,23 +135,26 @@
 ## ==================================================
 ## Start of analysis
 ## ==================================================
+## ==================================================
+## Start of analysis
+## ==================================================
 MAIN_NAME <- '[INFO] '
-TOOL_PATH <- getScriptPath()
-CSS_FILE  <- paste( TOOL_PATH, '/static/css/QDNAseq.css', sep="" )
-DECIMALS  <- 3
-WEB_LINK  <- 'http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html'
-PURE_CSS  <- 'http://yui.yahooapis.com/pure/0.5.0/pure-min.css'
-
 catMsg( "Starting QDNAseq wrapper" )	
 catMsg( "Loading R libraries" )
 catMsg( R.version.string )
 
+## supress msg to allow R to finish with non-error msg
 suppressWarnings( suppressMessages( library( QDNAseq, quietly = TRUE ) ) )
 suppressWarnings( suppressMessages( library( CGHcall, quietly = TRUE ) ) )
 
 ## only one param: the tmp config file
 cmdLineArgs <- commandArgs(TRUE)
 config      <- cmdLineArgs[1]
+TOOL_PATH   <- cmdLineArgs[2]
+CSS_FILE  <- paste( TOOL_PATH, '/static/css/QDNAseq.css', sep="" )
+DECIMALS  <- 3
+WEB_LINK  <- 'http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html'
+PURE_CSS  <- 'http://yui.yahooapis.com/pure/0.5.0/pure-min.css'
 
 ## sourcing the config file will load all input params
 ## many variables are imported via sourced "config"
diff -r 4db025c51b6e -r 0feb7fa37245 QDNAseq.xml
--- a/QDNAseq.xml	Fri Oct 24 07:06:55 2014 -0400
+++ b/QDNAseq.xml	Thu Nov 06 05:09:17 2014 -0500
@@ -14,6 +14,7 @@
   <command interpreter="Rscript"> 
     QDNAseq.R 
     $qdnaseq_cfg
+    \$QDNASEQ_PATH
   </command>
 
   <stdio>
diff -r 4db025c51b6e -r 0feb7fa37245 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Oct 24 07:06:55 2014 -0400
+++ b/tool_dependencies.xml	Thu Nov 06 05:09:17 2014 -0500
@@ -2,28 +2,27 @@
 <tool_dependency>
     
     <package name="samtools" version="0.1.18">
-        <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" prior_installation_required="TRUE" />
+        <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 
-    <!-- As soon as R 3_1_0 package works good, all dependencies will be set via "package_qdnaseq_1_0_5" -->
+    <!-- As soon as R 3_1_0 package works with all packages, all dependencies will be set via "package_qdnaseq_1_0_5" -->
     <!-- Currently these have to be manually installed by installing Bioconductor package "QDNAseq" -->
     
     <!--
     <package name="R" version="3.1.0">
-        <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" prior_installation_required="TRUE" />
+        <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" prior_installation_required="TRUE" />
     </package>
     -->
 
     <!--
     <package name="qdnaseq" version="1.0.5">
-        <repository name="package_qdnaseq_1_0_5" owner="stef"/>
+        <repository name="package_qdnaseq_1_0_5" owner="stef" prior_installation_required="TRUE"/>
     </package>
     -->
-
-    <!--
-    <action type="set_environment">
-        <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
-    </action>
-    -->
+    
+    <set_environment version="1.0">
+        <environment_variable action="set_to" name="QDNASEQ_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>
+    
     
 </tool_dependency>