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15
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1 # automate rnastar index generation
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2 # from existing fasta genomes using limited ram - cut genomeChrbinNbits down to 13, genomeSAindexNbases 12 genomeSAsparseD 1
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3
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4 INDEXROOT=/mnt/galaxyIndices/genomes
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5 # fix that, the list of genomes below and SOURCE below to suit your needs. This is for GVL august 2013
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6 for genome in Arabidopsis_thaliana_TAIR9 ce10 danRer7 dm3 hg19 hg_g1k_v37 mm9 phiX rn5 sacCer2 sacCer3 xenTro2
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7 do
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8 SOURCE=${INDEXROOT}/${genome}/seq/
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9 TARGET=${INDEXROOT}/${genome}/rnastar
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10 mkdir -p $TARGET
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11 cd $TARGET
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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
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13 done
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14
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15 echo "#add these lines TABS not spaces please to rnastar_indexes.loc in tool-data" > rnastar_indexes.loc
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16 for genome in Arabidopsis_thaliana_TAIR9 ce10 danRer7 dm3 hg19 hg_g1k_v37 mm9 phiX rn5 sacCer2 sacCer3 xenTro2
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17 do
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18 SOURCE=${INDEXROOT}/${genome}/seq/
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19 TARGET=${INDEXROOT}/${genome}/rnastar
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20 echo ${genome}'\t'${genome}'\t'${genome}'\t'/mnt/galaxyIndices/genomes/${genome}/rnastar >> rnastar_indexes.loc
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21 done
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