[med-svn] [Git][med-team/jellyfish1][master] Added autopkgtest

[Lance Lin (@linqigang)]

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 <LQi254 at protonmail.com>
+# 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

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View it on GitLab: https://salsa.debian.org/med-team/jellyfish1/-/commit/8b5dab5a5e6208c8b2d121b5b5ec8c2930cee185
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