# HG changeset patch
# User fubar
# Date 1377932763 14400
# Node ID 1e40b977aa58eaaa1b019add52a9986cd4b78c86
# Parent  9f65a7b3abeb028928ead1a315f4882370313dd6
Uploaded

diff -r 9f65a7b3abeb -r 1e40b977aa58 rgrnastar/prepStar.sh
--- a/rgrnastar/prepStar.sh	Tue Aug 20 22:39:23 2013 -0400
+++ b/rgrnastar/prepStar.sh	Sat Aug 31 03:06:03 2013 -0400
@@ -9,7 +9,7 @@
   TARGET=${INDEXROOT}/${genome}/rnastar
   mkdir -p $TARGET
   cd $TARGET
-/mnt/galaxy/tools/rnastar/2.3.0e/fubar/rgrnastar_203e/9425706f4e97/bin/STAR --runMode genomeGenerate --genomeDir $TARGET --genomeFastaFiles ${SOURCE}/${genome}.fa --runThreadN 2 genomeLoad=NoSharedMemory --genomeChrBinNbits 13 genomeSAindexNbases 12 genomeSAsparseD 1
+  /mnt/galaxy/tools/rnastar/2.3.0e/fubar/rgrnastar_203e/9425706f4e97/bin/STAR --runMode genomeGenerate --genomeDir $TARGET --genomeFastaFiles ${SOURCE}/${genome}.fa --runThreadN 2 genomeLoad=NoSharedMemory
 done
 
 echo "#add these lines TABS not spaces please to rnastar_indexes.loc in tool-data" > rnastar_indexes.loc
diff -r 9f65a7b3abeb -r 1e40b977aa58 rgrnastar/rg_rnaStar.xml
--- a/rgrnastar/rg_rnaStar.xml	Tue Aug 20 22:39:23 2013 -0400
+++ b/rgrnastar/rg_rnaStar.xml	Sat Aug 31 03:06:03 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="rna_star" name="RNA-STAR" version="0.22">
+<tool id="rna_star" name="RNA-STAR" version="0.23">
     <description>Gapped-read mapper for RNA-seq data</description>
     <requirements>
         <requirement type="package" version="2.3.0e">rnastar</requirement>
@@ -116,8 +116,8 @@
     </inputs>
 
     <outputs>
-       <data format="txt" name="output_log" label="${on_string}_{jobName}.log" from_work_dir="Log.final.out"/>
-       <data format="interval" name="chimeric_junctions" label="${on_string}_{jobName}_starchimjunc.bed" from_work_dir="Chimeric.out.junction">
+       <data format="txt" name="output_log" label="${on_string}_${jobName}.log" from_work_dir="Log.final.out"/>
+       <data format="interval" name="chimeric_junctions" label="${on_string}_${jobName}_starchimjunc.bed" from_work_dir="Chimeric.out.junction">
           <filter>(params['settingsType'] == 'full' and params['chim_segment_min'] > 0)</filter>
           <actions>
              <conditional name="refGenomeSource.genomeSource">