Mercurial > repos > bcclaywell > microbiome_pplacer_suite
diff preprocessing-wrapper.sh @ 3:221a97bf686d draft
Uploaded
author | bcclaywell |
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date | Wed, 25 Mar 2015 16:39:10 -0400 |
parents | d4690e65afcd |
children |
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--- a/preprocessing-wrapper.sh Thu Feb 26 19:31:20 2015 -0500 +++ b/preprocessing-wrapper.sh Wed Mar 25 16:39:10 2015 -0400 @@ -7,14 +7,3 @@ --deduplicated-sequences-file ${DEDUP_INFO} \ ${INPUT_SEQS} \ ${DEDUP_SEQS} - -# adapted from yapp/bin/refpkg_align -ref_sto=$(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" "${DEDUP_SEQS}" | grep -E '^#' - -esl-alimerge --dna --outformat afa "$ref_sto" "$sto" | \ - seqmagick convert --output-format fasta --dash-gap - "${ALIGNED_SEQS}"