comparison rgrnastar/prepStar.sh @ 8:6b232288f519 draft

Uploaded

7:9425706f4e97

# automate their generation f
# from existing fasta genomes
INDEXROOT=/data/ucsc
# fix that
for genome in hg19 hg18 mm9 mm10 rn4 rn5
do
  TARGET=${INDEXROOT}/${genome}/rnastar
  mkdir -p $TARGET
  cd $TARGET
  STAR --runMode genomeGenerate --genomeDir $TARGET --genomeFastaFiles ${TARGET}/$genome.fa --runThreadN 4
done

8:6b232288f519

# automate rnastar index generation
# from existing fasta genomes
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
  /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