Mercurial > repos > davidvanzessen > argalaxy_tools

changeset 7:c5cffbd8fe9d draft

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Uploaded
author davidvanzessen
date Thu, 30 Jul 2015 09:53:27 -0400
parents e61d06912e86
children 34d5e6df3247
files complete_immunerepertoire.xml igblast/igblast.sh tool_dependencies.xml
diffstat 2 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- 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" "$output" 2>&1
--- a/tool_dependencies.xml	Thu Jul 30 09:48:10 2015 -0400
+++ b/tool_dependencies.xml	Thu Jul 30 09:53:27 2015 -0400
@@ -17,7 +17,7 @@
                     <destination>$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>