# HG changeset patch
# User davidvanzessen
# Date 1438264407 14400
# Node ID c5cffbd8fe9dbd84cd9cd1ee3a498972cd1c52e6
# Parent  e61d06912e869459e94e3a7f29c27fab0c250cf6
Uploaded

diff -r e61d06912e86 -r c5cffbd8fe9d complete_immunerepertoire.xml
diff -r e61d06912e86 -r c5cffbd8fe9d igblast/igblast.sh
--- a/igblast/igblast.sh	Thu Jul 30 09:48:10 2015 -0400
+++ b/igblast/igblast.sh	Thu Jul 30 09:53:27 2015 -0400
@@ -10,6 +10,6 @@
 
 echo "$input $species $locus $output"
 
-java -jar igblastwrp.jar -cf -S $species -R $locus ${input} $PWD/blasted_output
+java -jar $IGBLASTWRP/igblastwrp.jar -cf -S $species -R $locus ${input} $PWD/blasted_output
 
 Rscript --verbose $dir/igblast.r "$PWD/blasted_output.L2.txt" "$output" 2>&1
diff -r e61d06912e86 -r c5cffbd8fe9d tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jul 30 09:48:10 2015 -0400
+++ b/tool_dependencies.xml	Thu Jul 30 09:53:27 2015 -0400
@@ -17,7 +17,7 @@
                     <destination>$INSTALL_DIR/</destination>
                 </action>
                 <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/</environment_variable>
+                    <environment_variable name="IGBLASTWRP" action="set_to">$INSTALL_DIR/</environment_variable>
                 </action>
             </actions>
         </install>