Mercurial > repos > bcclaywell > microbiome_pplacer_suite
view alignment-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 | 221a97bf686d |
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#!/bin/bash source $1 # adapted from yapp/bin/refpkg_align ref_sto=$(taxit rp ${REFPKG} aln_sto) profile=$(taxit rp ${REFPKG} profile) sto=$(mktemp -u).sto cmalign --cpu ${GALAXY_SLOTS:-4} -o "$sto" --sfile "${ALIGNED_SCORES}" --noprob --dnaout "$profile" "${INPUT_SEQS}" | grep -E '^#' esl-alimerge --dna --outformat afa "$ref_sto" "$sto" | \ seqmagick convert --output-format fasta --dash-gap - "${ALIGNED_SEQS}"