Mercurial > repos > davidvanzessen > mutation_analysis

diff wrapper.sh @ 12:257e98fd3b54 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Mon, 30 Mar 2015 05:06:45 -0400
parents 069419cccba4
children 8a40634fd4b3
line wrap: on
line diff
--- a/wrapper.sh	Thu Mar 26 10:16:20 2015 -0400
+++ b/wrapper.sh	Mon Mar 30 05:06:45 2015 -0400
@@ -15,9 +15,9 @@
 
 
 echo "identification"
-python $dir/gene_identification.py --input $PWD/summary.txt --output $PWD/annotatedsummary.txt
+python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/annotatedsummary.txt
 echo "merging"
-Rscript $dir/merge_and_filter.r $PWD/annotatedsummary.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/merged.txt $outdir/unmatched.txt
+Rscript $dir/merge_and_filter.r $outdir/annotatedsummary.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/merged.txt $outdir/unmatched.txt
 
 genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm"
 echo "R mutation analysis"