star_genome_generate_cmd = str("STAR --runThreadN " +
args.nthreads +
" --runMode genomeGenerate" +
" --genomeDir star_genome_idx " +
" --genomeFastaFiles {} ".format(st_fa_path) +
" --genomeSAindexNbases 8 " + # as per A. Dobin
" --sjdbGTFfile {} ".format(st_gtf_path) +
" --sjdbOverhang {} ".format(args.sjdbOverhang) +
" --limitGenomeGenerateRAM {}".format(args.maxram) )
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>> Brian J. Haas
>> The Broad Institute
>> http://broadinstitute.org/~bhaas
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The Genome Analysis Toolkit (GATK) v3.8-0-ge9d806836, Compiled 2017/07/28 21:26:50
Copyright (c) 2010-2016 The Broad Institute
For support and documentation go to https://software.broadinstitute.org/gatk
[Mon Feb 12 21:19:16 EST 2018] Executing on Mac OS X 10.11.6 x86_64
Java HotSpot(TM) 64-Bit Server VM 1.8.0_102-b14
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>>
>> --
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>> Brian J. Haas
>> The Broad Institute
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--
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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas
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