Mercurial > repos > davidvanzessen > mutation_analysis

changeset 15:8a40634fd4b3 draft

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Uploaded
author davidvanzessen
date Mon, 30 Mar 2015 05:11:25 -0400
parents 6f8392d090bd
children 2bb24ebbbc38
files tool_dependencies.xml wrapper.sh
diffstat 2 files changed, 3 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Mon Mar 30 05:08:28 2015 -0400
+++ b/tool_dependencies.xml	Mon Mar 30 05:11:25 2015 -0400
@@ -12,7 +12,7 @@
 								<destination>$INSTALL_DIR</destination>
 							</action>
 							<action type="set_environment">
-								<environment_variable name="BLASTN" action="set_to">$INSTALL_DIR</environment_variable>
+								<environment_variable name="BLASTN_DIR" action="set_to">$INSTALL_DIR</environment_variable>
 							</action>
             </actions>
         </install>
--- a/wrapper.sh	Mon Mar 30 05:08:28 2015 -0400
+++ b/wrapper.sh	Mon Mar 30 05:11:25 2015 -0400
@@ -13,6 +13,8 @@
 cat $PWD/files/*/8_* > $PWD/mutationstats.txt
 cat $PWD/files/*/10_* > $PWD/hotspots.txt
 
+echo "${BLASTN_DIR}"
+
 
 echo "identification"
 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/annotatedsummary.txt