Mercurial > repos > fubar > rgrnastar_203e
changeset 8:6b232288f519 draft
Uploaded
| author | fubar |
|---|---|
| date | Sat, 10 Aug 2013 07:02:37 -0400 |
| parents | 9425706f4e97 |
| children | c3ac5a2a2bfb |
| files | rgrnastar/prepStar.sh rgrnastar/tool-data/rnastar_indices.loc.sample |
| diffstat | 2 files changed, 8 insertions(+), 11 deletions(-) [+] |
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--- 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
--- a/rgrnastar/tool-data/rnastar_indices.loc.sample Sat Aug 10 01:42:26 2013 -0400 +++ b/rgrnastar/tool-data/rnastar_indices.loc.sample Sat Aug 10 07:02:37 2013 -0400 @@ -7,10 +7,5 @@ # #<unique_build_id> <dbkey> <display_name> <file_base_path> # -hg19 hg19 hg19 full /data/ucsc/hg19/rnastar -hg18 hg18 hg18 full /data/ucsc/hg18/rnastar -mm9 mm9 mm9 full /data/ucsc/mm9/rnastar -mm10 mm10 mm10 full /data/ucsc/mm10/rnastar -rn4 rn4 rn4 full /data/ucsc/rn4/rnastar -rn5 rn5 rn5 full /data/ucsc/rn5/rnastar +#hg19 hg19 hg19 full /mnt/galaxyIndices/genomes/hg19/rnastar