# HG changeset patch
# User fubar
# Date 1376139492 14400
# Node ID c3ac5a2a2bfbe0679505648d7ad9bdd214f842b8
# Parent  6b232288f51946c88a65b9a7973e29d7544dc177
Uploaded

diff -r 6b232288f519 -r c3ac5a2a2bfb rgrnastar/prepStar.sh
--- a/rgrnastar/prepStar.sh	Sat Aug 10 07:02:37 2013 -0400
+++ b/rgrnastar/prepStar.sh	Sat Aug 10 08:58:12 2013 -0400
@@ -1,5 +1,6 @@
 # automate rnastar index generation
-# from existing fasta genomes
+# from existing fasta genomes using limited ram - cut genomeChrbinNbits down to 13, genomeSAindexNbases 12 genomeSAsparseD 1
+
 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
@@ -8,7 +9,13 @@
   TARGET=${INDEXROOT}/${genome}/rnastar
   mkdir -p $TARGET
   cd $TARGET
-  /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
+/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
 done
 
+echo "#add these lines TABS not spaces please to rnastar_indexes.loc in tool-data" > rnastar_indexes.loc
+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
+  echo ${genome}'\t'${genome}'\t'${genome}'\t'/mnt/galaxyIndices/genomes/${genome}/rnastar >> rnastar_indexes.loc
+done