Mercurial > repos > bcclaywell > microbiome_pplacer_suite

diff preprocessing-wrapper.sh @ 3:221a97bf686d draft
Uploaded
author: bcclaywell
date: Wed, 25 Mar 2015 16:39:10 -0400
parents: d4690e65afcd
--- 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}"