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view alignment-wrapper.sh @ 7:b6ece07bec6a draft

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planemo upload commit 45906ba522c7c319067e93d5cd5d7161223c3336
author bcclaywell
date Mon, 12 Oct 2015 15:59:59 -0400
parents 221a97bf686d
children
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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}"