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#!/bin/bash
set -e
pkg=changeo
CUR_DIR=`pwd`
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
cp ${CUR_DIR}/debian-tests-data/* -a "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
gunzip -r *
MakeDb.py imgt -i S43_atleast-2.txz -s S43_atleast-2.fasta
echo "a3e982b96df29477a5eccdb19e5c2abe S43_atleast-2_db-pass.tsv" >> checksums
CreateGermlines.py -d S43_atleast-2_db-pass.tsv -g dmask -r IMGT_Human_IGHV.fasta IMGT_Human_IGHD.fasta IMGT_Human_IGHJ.fasta
echo "488ab5a17d06dc1e790e3c444b88f300 S43_atleast-2_db-pass_germ-pass.tsv" >> checksums
ParseDb.py select -d S43_atleast-2_db-pass.tsv -f productive -u T
echo "ab2391a45c16207ad6cb720a146c34bf S43_atleast-2_db-pass_parse-select.tsv" >> checksums
# Hint: there was a checksum diff between version 1.2 and 1.3
# After inspecting the real diff with `wdiff -3` it turned out that there was only a minor text change
# Thus the checksums were refreshed
md5sum --check checksums
#Generates a randomised grouping
DefineClones.py -d S43_atleast-2_db-pass.tsv --act set --model ham --norm len --dist 0.16
BuildTrees.py -d S43_atleast-2_db-pass_clone-pass.tsv --outname ex --log ex.log --collapse --sample 3000 --clean all --nproc 1
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