# HG changeset patch
# User rnateam
# Date 1423064684 18000
# Node ID b21be04f52e46bd47f27b986ef65277c6c3bfbcc
# Parent  eaac585f172ae006c9a88a5169daf079ce055dd0
Uploaded

diff -r eaac585f172a -r b21be04f52e4 mirdeep2.xml
--- a/mirdeep2.xml	Tue Jan 27 09:06:24 2015 -0500
+++ b/mirdeep2.xml	Wed Feb 04 10:44:44 2015 -0500
@@ -60,20 +60,20 @@
     -b $min_score_cutoff
     $disable_randfold
     
-    ; cp result*.bed result.bed 2> /dev/null
-    ; cp result*.csv result.csv 2> /dev/null
-    ; cp mirdeep_runs/run*/output.mrd . 2> /dev/null
-    ; cp mirdeep_runs/run*/survey.csv . 2> /dev/null
+    ; mv result*.bed result.bed 2> /dev/null
+    ; mv result*.csv result.csv 2> /dev/null
+    ; mv mirdeep_runs/run*/output.mrd . 2> /dev/null
+    ; mv mirdeep_runs/run*/survey.csv . 2> /dev/null
     
     ## html output
     ;
-    cp result*.html $html 2> /dev/null
+    mv result*.html $html 2> /dev/null
     
     ## move pdf directory to be accessible from the new index.html
     ;
     mkdir -p $html.files_path 2> /dev/null
     ;
-    cp -R pdfs* $html.files_path 2> /dev/null
+    mv pdfs* $html.files_path 2> /dev/null
     
 ]]>
     </command>
diff -r eaac585f172a -r b21be04f52e4 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jan 27 09:06:24 2015 -0500
+++ b/tool_dependencies.xml	Wed Feb 04 10:44:44 2015 -0500
@@ -1,33 +1,33 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="perl" version="5.18.1">
-      <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="perl" version="5.18.1">
+        <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="bowtie" version="0.12.7">
-      <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="vienna_rna" version="1.8.5">
-      <repository changeset_revision="54e961ee33d4" name="package_vienna_rna_1_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="6757330f89cd" name="package_vienna_rna_1_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="pdf_api2" version="2.023">
-      <repository changeset_revision="b9b7fadfdb69" name="package_perl_pdf_api2_2_023" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="b9b7fadfdb69" name="package_perl_pdf_api2_2_023" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="randfold" version="2.0">
-      <repository changeset_revision="b34d2c942c79" name="package_randfold_2_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="b34d2c942c79" name="package_randfold_2_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="mirdeep2_quantifier" version="2.0">
-      <repository changeset_revision="2c039fc73f1f" name="mirdeep2_quantifier" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="2c039fc73f1f" name="mirdeep2_quantifier" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="mirdeep2" version="2.0">
-      <install version="1.0">
-          <actions>
-              <action type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/miRDeep2/miRDeep2.tar.gz</action>
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/miRDeep2/miRDeep2.tar.gz</action>
                 <action type="move_directory_files">
-                  <source_directory>.</source_directory>
+                    <source_directory>.</source_directory>
                     <destination_directory>$INSTALL_DIR</destination_directory>
                 </action>
                 <action type="set_environment">
-                  <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
                 </action>
             </actions>
         </install>