Mercurial > repos > bcclaywell > microbiome_pplacer_suite

view pplacer-wrapper.sh @ 6:3c50a937d7c1 draft

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author bcclaywell
date Wed, 15 Apr 2015 19:14:23 -0400
parents d4690e65afcd
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#!/bin/bash

source $(dirname $0)/util.sh
source $1

QUERY_SEQS=$(extify fasta ${QUERY_SEQS})
PPLACER_DEFAULT_ARGS="-j ${GALAXY_SLOTS:-4} -p --inform-prior --prior-lower 0.01 --map-identity"

pplacer \
    ${PPLACER_DEFAULT_ARGS} \
    -c ${REFPKG} \
    -o ${PLACED_SEQS} \
    ${QUERY_SEQS}