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kbaseattic / assembly

An extensible framework for genome assembly.
MIT License
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Incorporate MEGAHIT into recipes and human readable command logging for subcommands #294

Closed levinas closed 9 years ago

levinas commented 9 years ago

Converts

['/mnt/nfs/ar-src/arast.dev/third_party/megahit/megahit', '--cpu-only', '--num-cpu-threads', '32', '-l', '512', '-m', '1051588452352', '--input-cmd', u'cat /mnt/data
/dmachi_patricbrc_org/4/raw/p1.fq /mnt/data/dmachi_patricbrc_org/4/raw/p2.fq', '-o', u'/mnt/data/dmachi_patricbrc_org/4/4/megahit_71f46771-8229-4ed3-8af0-30851a6cf345/megahit']

to

Command: megahit --cpu-only --num-cpu-threads 32 -l 512 -m 1051588452352 --input-cmd "cat p1.fq p2.fq" -o megahit

Related to #244