# HG changeset patch
# User stef
# Date 1414754033 14400
# Node ID 4efd258b33d967bf63991e31ca9e3b0c2eaa95db
# Parent  238a698f7904b594a6079b4e22638d9f954fc7e8
Uploaded

diff -r 238a698f7904 -r 4efd258b33d9 QDNAseq.R
--- a/QDNAseq.R	Mon Oct 27 05:38:16 2014 -0400
+++ b/QDNAseq.R	Fri Oct 31 07:13:53 2014 -0400
@@ -135,9 +135,13 @@
 ## ==================================================
 ## Start of analysis
 ## ==================================================
+cmdLineArgs <- commandArgs(TRUE)
+config      <- cmdLineArgs[1]
+installDir  <- cmdLineArgs[2]
+
 MAIN_NAME <- '[INFO] '
 TOOL_PATH <- getScriptPath()
-CSS_FILE  <- paste( TOOL_PATH, '/static/css/QDNAseq.css', sep="" )
+CSS_FILE  <- paste( installDir, '/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'
@@ -146,20 +150,9 @@
 catMsg( "Loading R libraries" )
 catMsg( R.version.string )
 
-packs <- c( "limma", "marray", "CGHbase", "impute", "DNAcopy", "CGHcall" )
-for ( pack in packs ){
-	catMsg( c("Loading ", pack) )
-	library( pack )
-}
-
-## 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]
-
 ## sourcing the config file will load all input params
 ## many variables are imported via sourced "config"
 source( config )
diff -r 238a698f7904 -r 4efd258b33d9 QDNAseq.xml
--- a/QDNAseq.xml	Mon Oct 27 05:38:16 2014 -0400
+++ b/QDNAseq.xml	Fri Oct 31 07:13:53 2014 -0400
@@ -3,8 +3,8 @@
   <requirements>
     
     <!-- R 3.1.0 dependency will be used instead when available, now default R is used, see command -->
-    <requirement type="package" version="3.1.0">R</requirement>
-    <requirement type="package" version="1.0.5">qdnaseq</requirement>
+    <!-- <requirement type="package" version="3.1.0">R</requirement> -->
+    <!-- <requirement type="package" version="1.0.5">qdnaseq</requirement> -->
     <requirement type="package" version="0.1.18">samtools</requirement>
   </requirements>
 
@@ -14,6 +14,7 @@
   <command interpreter="Rscript"> 
     QDNAseq.R 
     $qdnaseq_cfg
+    $INSTALL_DIR
   </command>
 
   <stdio>
diff -r 238a698f7904 -r 4efd258b33d9 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Oct 27 05:38:16 2014 -0400
+++ b/tool_dependencies.xml	Fri Oct 31 07:13:53 2014 -0400
@@ -2,24 +2,28 @@
 <tool_dependency>
     
     <package name="samtools" version="0.1.18">
-        <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" prior_installation_required="TRUE" />
     </package>
 
     <!-- As soon as R 3_1_0 package works good, 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" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" prior_installation_required="TRUE" />
     </package>
-    
-    <package name="qdnaseq" version="1.0.5">
-        <repository changeset_revision="8473e3b3c386" name="package_qdnaseq_1_0_5" owner="stef" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
+    -->
 
     <!--
+    <package name="qdnaseq" version="1.0.5">
+        <repository name="package_qdnaseq_1_0_5" owner="stef"/>
+    </package>
+    -->
+
+    
     <action type="set_environment">
-        <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+        <environment_variable name="INSTALL_DIR" action="prepend_to">$INSTALL_DIR</environment_variable>
     </action>
-    -->
+    
     
 </tool_dependency>