Lance Lin pushed to branch master at Debian Med / jellyfish1
Commits: 8b5dab5a by Lance Lin at 2022-03-24T19:18:41+07:00 Added autopkgtest - - - - - 2 changed files: - + debian/tests/control - + debian/tests/run-unit-test Changes: ===================================== debian/tests/control ===================================== @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,56 @@ +#!/bin/sh + +# Author: Lance Lin <[email protected]> +# Date: 24 March 2022 +# File: run-unit-test +# Purpose: run a simple-unit test for the jellyfish1 package + +set -e + +if [ "${AUTOPKGTEST_TMP}" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM +fi +cd "${AUTOPKGTEST_TMP}" + +echo "run-unit-test: generating sample data" + +# This is sample.fasta from the lagan package +# Source is at: https://salsa.debian.org/med-team/lagan +cat <<EOF > sample.fasta +>sample1 +GGCATGTCCAGAAAATCCAAGTGCCTCTTCCTCTTGATCTTCTCCAACGATGTCCAGA +AAATCCAAGTGCCTCATTCCTCTTGATCTTCTCCAGGCATGTCCAGAAAATCCAAGTG +CCTCTTCCTCTCTGATCTTCTCCTCGGTTGGTCCAGAAAATCCAAGTGCCTCTTCCTC +TTGATCTTCTCCAGAAATGTCCAGAAAATCCAAGTAGCCTCTTCCTCTTGATCGGCTC +CAGAAATGTCCAGAAAAATCCAAGTGCCTCTTCCTCTTGATCGGCTCCATAAATGTCC +AGAAAATCCAACGTGCCTCTTCCTCTTGATCGGCTCCAGAAATGTCCAGAAATATCCA +AGTGCCTCTTCCTCTTGATCGGCTCCTTA +>sample2 +CGATCCCAAATCCAAGTGCCTCAGAGTCTACTTGATCTTCAATTCAGATCCCAAATCC +AAGTGCCTCAGAGTCTACTTGAATCTTCTATCGGGTCCCAAATCCAAGTGCCTCAGAG +TCTACTTGATCTTCTCTCTCGATCCCATATCCAAGTGCCTCCTAGAGTCTACTTGATC +TTCTCGATAACCAAAATCCAAGTGCCTCAGAGTCTACTTCACTCTTCTCGACTAACCC +AAATCCAAGTGCCTCAGATGAGTCTACTTCCTCTTCTCATAACTCAAATCCAAGTGCC +TCAGAGTCTAACTTCCTCTTCTCGAATAACCCAAATCCAAGTGCCTCAGAGTGTCTAC +TTCCTCTTCTCG +>sample3 +TACCCAAATCCAAGTGCCTCAGCGTCTAATAAAACAAGTCTTGATCTTCAACTCCTCC +CAAATCCAAGTGCAACCTCAGCCGCTAATAAAAAGTCTTGATCTTCTCGCGTCCGGCA +AATCCAAGTGCCTCAGCGCTAATAAAAAGTCTTGATCTTCTCGGGAGTCCCAAATCCA +AGTGCCTCAGCGCTAATAAAAAGTCTTGATCTTCTCGGAGGAACAACAAATCCAAGTG +CCTCAAGCGCTAATAAAAAGTCCCGATCTTCTCGTGACAATACAAATCCAAGTGCCTC +AGCGCTAATAAAAAGTCCCGATCTTCTCCCGTGTAAACAAATCCAAGTGCCTCAGCGC +TAATAAAAAGTCCCGATCTTCTCTGGTAACACAACAAATCCAAGTCACGCCTCAGATA +CGCTAATAAAAAGTCCCGATCTTCTC +EOF + +echo "run-unit-test: generating md5 sums for verification" +echo "38a6b3803a6893101435b919d7bc7605 output_0" >> checksums + +echo "run-unit-test: running jellyfish1" +jellyfish1 count -m 22 -o output -c 3 -s 10000000 -t 32 sample.fasta + +echo "run-unit-test: verifying md5 checksums" +md5sum --check checksums + View it on GitLab: https://salsa.debian.org/med-team/jellyfish1/-/commit/8b5dab5a5e6208c8b2d121b5b5ec8c2930cee185 -- View it on GitLab: https://salsa.debian.org/med-team/jellyfish1/-/commit/8b5dab5a5e6208c8b2d121b5b5ec8c2930cee185 You're receiving this email because of your account on salsa.debian.org.
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