Mercurial > repos > fubar > rgrnastar_203e

comparison rgrnastar/prepStar.sh @ 14:1e40b977aa58 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author fubar
date Sat, 31 Aug 2013 03:06:03 -0400
parents c3ac5a2a2bfb
children
comparison
equal deleted inserted replaced
13:9f65a7b3abeb 14:1e40b977aa58
7 do 7 do
8 SOURCE=${INDEXROOT}/${genome}/seq/ 8 SOURCE=${INDEXROOT}/${genome}/seq/
9 TARGET=${INDEXROOT}/${genome}/rnastar 9 TARGET=${INDEXROOT}/${genome}/rnastar
10 mkdir -p $TARGET 10 mkdir -p $TARGET
11 cd $TARGET 11 cd $TARGET
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 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
13 done 13 done
14 14
15 echo "#add these lines TABS not spaces please to rnastar_indexes.loc in tool-data" > rnastar_indexes.loc 15 echo "#add these lines TABS not spaces please to rnastar_indexes.loc in tool-data" > rnastar_indexes.loc
16 for genome in Arabidopsis_thaliana_TAIR9 ce10 danRer7 dm3 hg19 hg_g1k_v37 mm9 phiX rn5 sacCer2 sacCer3 xenTro2 16 for genome in Arabidopsis_thaliana_TAIR9 ce10 danRer7 dm3 hg19 hg_g1k_v37 mm9 phiX rn5 sacCer2 sacCer3 xenTro2
17 do 17 do