--- a/rgrnastar/prepStar.sh	Sat Aug 10 01:42:26 2013 -0400
+++ b/rgrnastar/prepStar.sh	Sat Aug 10 07:02:37 2013 -0400
@@ -1,12 +1,14 @@
-# automate their generation f
+# automate rnastar index generation
 # from existing fasta genomes
-INDEXROOT=/data/ucsc
-# fix that
-for genome in hg19 hg18 mm9 mm10 rn4 rn5
+INDEXROOT=/mnt/galaxyIndices/genomes
+# fix that, the list of genomes below and SOURCE below to suit your needs. This is for GVL august 2013
+for genome in Arabidopsis_thaliana_TAIR9  ce10  danRer7  dm3  hg19  hg_g1k_v37  mm9  phiX  rn5  sacCer2  sacCer3  xenTro2
 do
+  SOURCE=${INDEXROOT}/${genome}/seq/
   TARGET=${INDEXROOT}/${genome}/rnastar
   mkdir -p $TARGET
   cd $TARGET
-  STAR --runMode genomeGenerate --genomeDir $TARGET --genomeFastaFiles ${TARGET}/$genome.fa --runThreadN 4
+  /mnt/galaxy/tools/rnastar/2.3.0e/fubar/rgrnastar_203e/33b5c8dc8e60/bin/STAR --runMode genomeGenerate --genomeDir $TARGET --genomeFastaFiles ${SOURCE}/seq/${genome}.fa --runThreadN 2 genomeLoad=NoSharedMemory
+ --genomeChrBinNbits 12
 done