Nilesh Patra pushed to branch master at Debian Med / pal2nal
Commits: 2f3ccdb7 by Nilesh Patra at 2020-07-01T23:57:53+05:30 Add autopkgtests - - - - - 40326fdc by Nilesh Patra at 2020-07-01T23:58:05+05:30 Add relevant examples - - - - - 412bc28b by Nilesh Patra at 2020-07-01T23:58:45+05:30 Bump compat version to 13 - - - - - 3e9f13be by Nilesh Patra at 2020-07-01T23:59:27+05:30 Add "Rules-Requires-Root:no" - - - - - 9b31152b by Nilesh Patra at 2020-07-02T00:03:49+05:30 Update metadata URLs - - - - - 1be1df53 by Nilesh Patra at 2020-07-01T18:42:43+00:00 Bump standards version to 4.5.0 - - - - - 8 changed files: - − debian/compat - debian/control - debian/examples - + debian/tests/README - + debian/tests/control - + debian/tests/run-unit-test - + debian/tests/test.expected - debian/upstream/metadata Changes: ===================================== debian/compat deleted ===================================== @@ -1 +0,0 @@ -11 ===================================== debian/control ===================================== @@ -4,11 +4,12 @@ Uploaders: Pjotr Prins <[email protected]>, Steffen Moeller <[email protected]> Section: science Priority: optional -Build-Depends: debhelper (>= 11~) -Standards-Version: 4.2.1 +Build-Depends: debhelper-compat (= 13) +Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/pal2nal Vcs-Git: https://salsa.debian.org/med-team/pal2nal.git Homepage: http://www.bork.embl.de/pal2nal +Rules-Requires-Root: no Package: pal2nal Architecture: all ===================================== debian/examples ===================================== @@ -1,2 +1,3 @@ test.aln test.nuc +debian/tests/test.expected ===================================== debian/tests/README ===================================== @@ -0,0 +1,5 @@ +Tests for pa2nal +================= + +The expected output has been generated by running the command: + pal2nal.pl test.aln test.nuc -output paml -nogap > test.expected 2>/dev/null ===================================== debian/tests/control ===================================== @@ -0,0 +1,4 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr + ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,20 @@ +#!/bin/bash +set -e + +pkg=pal2nal + +if [ "${AUTOPKGTEST_TMP}" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM +fi + +cp /usr/share/doc/${pkg}/examples/* -a "${AUTOPKGTEST_TMP}" + +cd "${AUTOPKGTEST_TMP}" +gunzip -r * + +echo 'Test' +pal2nal.pl test.aln test.nuc -output paml -nogap > res 2>/dev/null +diff -u res test.expected +echo 'PASS' + ===================================== debian/tests/test.expected ===================================== @@ -0,0 +1,21 @@ + 2 531 +BC070280 +CTAAACTGCATCGTCGCTGTGTCCCAGAACATGGGCATCGGCAAGAACGGGGACCTGCCC +CCACCGCTCAGGAATGAATTCTTCCAGAGAATGACCACAACCTCTTCAGTAGAAGGTAAA +CAGAATCTGGTGATTATGGGTAAGAAGACCTGGTTCTCCATTCCTGAGAAGAATCGACCT +TTAAAGGGTAGAATTAATTTAGTTCTCAGCAGAGAACTCAAGGAACCTCCACAAGGAGCT +CATTTTCTTTCCAGTCTAGATGATGCCTTAAAACTTACTGAACAACCAGAATTAGCAAAT +AAAGTAGACATGCTCTGGATAGTTGGTGGCAGTTCTGTTTATAAGGAAGCCATGAATGGC +CATCTTAAACTATTTGTGACAAGGATCATGCAAGACTTTGAAAGTGACACGTTTTTTCCA +GAAATTGATTTGGAGAAATATAAACTTCTGCCAGAATACCCAGGTGTTCTCTCTGATGTC +CAGGAGGAGAAAGGCATTAAGTACAAATTTGAAGTATATGAGAAGAATGAT +pseudogene +CTAAACTGCATTGTCAATGATTCCCAGAAGATGGGCATCATCAGGAATGGGGACCTGCCC +CCTCAGCTCAAAAATAAATTCTTCCAAAGAATGACCACACCCTCTTCAGCAGAGGGTAAA +GAAAATTTAGTATTTTTAATTAGGAAGAACTGGTTCTCGATTACTGAGAAGAATCAACCT +TTAAAGTATATAATTAATTTAGTTGTCAGTAGAGAATCCAAGGAACCACCGCAAAGACCT +CCTTTTCTTGACAGTCTGGGTGATGCCTTAAAACGTATTGAGCAACTAAAATTAGCAAAT +AAACAAGACGTGTTTTTTACAGTGGGAGGCAGTTCTGTTTATAAGGAATCCATGAATGAC +CATTTTAAACTATTTGTGACATGGATCATGCAGGACTTTCAAAGTGACACGTTTTTTCCT +GAAGGTGATTTAGAGAAATATAAACTTCTCCCAGAATACCCAGGTGTTGTCTCTGATGTG +GAGGAGGAGAAAGGCATTAAGTACAAATTTGAAGTATATGAAAAGAATGAT ===================================== debian/upstream/metadata ===================================== @@ -9,9 +9,9 @@ Reference: Pages: W609-W612 DOI: 10.1093/nar/gkl315 PMID: 16845082 - URL: http://nar.oxfordjournals.org/content/34/suppl_2/W609 + URL: https://academic.oup.com/nar/article/34/suppl_2/W609/2505720 eprint: > - http://nar.oxfordjournals.org/content/34/suppl_2/W609.full.pdf+html + https://academic.oup.com/nar/article-pdf/34/suppl_2/W609/7623711/gkl315.pdf Registry: - Name: OMICtools Entry: OMICS_20386 View it on GitLab: https://salsa.debian.org/med-team/pal2nal/-/compare/13cafd11742542d50c8b11f7b52d6c2b26023161...1be1df53e3e7d71d2eb07a5c4826e628a5d8578b -- View it on GitLab: https://salsa.debian.org/med-team/pal2nal/-/compare/13cafd11742542d50c8b11f7b52d6c2b26023161...1be1df53e3e7d71d2eb07a5c4826e628a5d8578b You're receiving this email because of your account on salsa.debian.org.
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