Saira Hussain pushed to branch master at Debian Med / norsnet
Commits: a582802b by Saira Hussain at 2019-07-31T10:31:25Z Add basic test functionality - - - - - 8e8064ec by Saira Hussain at 2019-07-31T10:33:00Z Bump changelog - - - - - 4 changed files: - debian/changelog - + debian/examples - + debian/tests/control - + debian/tests/run-unit-tests Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,12 @@ +norsnet (1.0.17-5) UNRELEASED; urgency=medium + + * Team upload. + + [Saira Hussain] + * Add unit tests + + -- Saira Hussain <[email protected]> Wed, 31 Jul 2019 11:31:56 +0100 + norsnet (1.0.17-4) unstable; urgency=medium * pp-popularity-contest only suggested ===================================== debian/examples ===================================== @@ -0,0 +1 @@ +examples/* ===================================== debian/tests/control ===================================== @@ -0,0 +1,3 @@ +Tests: run-unit-tests +Depends: @ +Restrictions: allow-stderr ===================================== debian/tests/run-unit-tests ===================================== @@ -0,0 +1,40 @@ +#!/bin/bash +set -e + +pkg=mcl + +if [ "${AUTOPKGTEST_TMP}" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + # Double quote below to expand the temporary directory variable now versus + # later is on purpose. + # shellcheck disable=SC2064 +# trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM +fi + +cp /usr/share/doc/${pkg}/examples/* -a "${AUTOPKGTEST_TMP}" + +cd "${AUTOPKGTEST_TMP}" +gunzip -r * + +# Just for debugging +set -x + +#Generation of protein families +mcxload -abc protein_graphs.txt --stream-mirror --stream-neg-log10 -stream-tf 'ceil(200)' -o protein_graphs.mci -write-tab protein_graphs.tab + +mcl protein_graphs.mci -I 2 + +mcxdump -icl out.protein_graphs.mci.I20 -tabr protein_graphs.tab -o clusters.protein_graphs.mci.I20 + +#Building clusters of genomes +mcxload -abc genome_graphs.txt --stream-mirror -o genome_graphs.mci -write-tab genome_graphs.tab + +mcl genome_graphs.mci -I 1.2 + +mcl genome_graphs.mci -I 2 +mcl genome_graphs.mci -I 4 +mcl genome_graphs.mci -I 6 +mcxdump -icl out.genome_graphs.mci.I12 -tabr genome_graphs.tab -o clusters.genome.mci.I12 +mcxdump -icl out.genome_graphs.mci.I20 -tabr genome_graphs.tab -o clusters.genome.mci.I20 +mcxdump -icl out.genome_graphs.mci.I40 -tabr genome_graphs.tab -o clusters.genome.mci.I40 +mcxdump -icl out.genome_graphs.mci.I60 -tabr genome_graphs.tab -o clusters.genome.mci.I60 View it on GitLab: https://salsa.debian.org/med-team/norsnet/compare/bbd49b7bfaef84ca1cea23383129893a16d1617d...8e8064ec462d3e8706dc05de0ebd805c824a3477 -- View it on GitLab: https://salsa.debian.org/med-team/norsnet/compare/bbd49b7bfaef84ca1cea23383129893a16d1617d...8e8064ec462d3e8706dc05de0ebd805c824a3477 You're receiving this email because of your account on salsa.debian.org.
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