Mercurial > repos > fubar > rgrnastar_203e
changeset 9:c3ac5a2a2bfb draft
Uploaded
| author | fubar |
|---|---|
| date | Sat, 10 Aug 2013 08:58:12 -0400 |
| parents | 6b232288f519 |
| children | 1ce3d6f45fbc |
| files | rgrnastar/prepStar.sh |
| diffstat | 1 files changed, 10 insertions(+), 3 deletions(-) [+] |
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--- 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