Mercurial > repos > bcclaywell > microbiome_pplacer_suite
view preclassification-wrapper.sh @ 6:3c50a937d7c1 draft
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author | bcclaywell |
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date | Wed, 15 Apr 2015 19:14:23 -0400 |
parents | 5f0648f799a9 |
children |
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#!/bin/bash source $(dirname $0)/util.sh source $1 PLACED_SEQS=$(extify jplace ${PLACED_SEQS}) NBC_SEQS=$(extify fasta ${NBC_SEQS}) guppy redup \ -m \ -d ${DEDUP_INFO} \ -o ${REDUPED_SEQS} \ ${PLACED_SEQS} REDUPED_SEQS=$(extify jplace ${REDUPED_SEQS}) rppr prep_db \ -c ${REFPKG} \ --sqlite ${CLASS_DB} guppy classify \ -c ${REFPKG} \ -j ${GALAXY_SLOTS:-4} \ --pp \ --sqlite ${CLASS_DB} \ --classifier hybrid2 \ --nbc-sequences ${NBC_SEQS} \ ${PLACED_SEQS} multiclass_concat.py --dedup-info ${DEDUP_INFO} ${CLASS_DB}