Nilesh Patra pushed to branch master at Debian Med / pscan-tfbs
Commits: 006c8c8c by Nilesh Patra at 2020-08-12T11:39:29+00:00 Add autopkgtests - - - - - 8d5eb220 by Nilesh Patra at 2020-08-12T11:39:41+00:00 Install relevant examples - - - - - bd0bc2fb by Nilesh Patra at 2020-08-12T17:14:06+05:30 Drop compat, switch to debhelper compat version 13 - - - - - 83d2bdab by Nilesh Patra at 2020-08-12T17:14:37+05:30 Add "Rules-Requires-Root:no" - - - - - 2763d037 by Nilesh Patra at 2020-08-12T17:20:03+05:30 Add hardening options - - - - - 7 changed files: - − debian/compat - debian/control - debian/examples - debian/rules - + debian/tests/control - + debian/tests/run-unit-test - + debian/tests/sample.fasta Changes: ===================================== debian/compat deleted ===================================== @@ -1 +0,0 @@ -10 ===================================== debian/control ===================================== @@ -3,12 +3,13 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Steffen Moeller <[email protected]> Section: science Priority: optional -Build-Depends: debhelper (>= 10), +Build-Depends: debhelper-compat (= 13), libgsl-dev -Standards-Version: 4.3.0 +Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/pscan-tfbs Vcs-Git: https://salsa.debian.org/med-team/pscan-tfbs.git Homepage: http://www.beaconlab.it/pscan +Rules-Requires-Root: no Package: pscan-tfbs Architecture: any ===================================== debian/examples ===================================== @@ -1 +1,2 @@ example_matrix_file.wil +debian/tests/sample.fasta ===================================== debian/rules ===================================== @@ -3,12 +3,13 @@ export DH_VERBOSE=1 -include /usr/share/dpkg/buildtools.mk +export DEB_BUILD_MAINT_OPTIONS = hardening=+all CXXFLAGS += -flto LDFLAGS += -Wl,-flto %: - dh $@ + dh $@ override_dh_auto_build: $(CXX) $(CXXFLAGS) pscan.cpp -o pscan $(LDFLAGS) -lgslcblas -lgsl ===================================== debian/tests/control ===================================== @@ -0,0 +1,4 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr + ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,25 @@ +#!/bin/bash +set -e + +pkg=pscan-tfbs + +if [ "${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 1' +pscan-tfbs -p sample.fasta -l example_matrix_file.wil +cat sample.short_matrix +echo 'PASS' + +echo 'Test 2' +pscan-tfbs -p sample.fasta -l example_matrix_file.wil -N NFY +cat sample.short_matrix +echo 'PASS' + ===================================== debian/tests/sample.fasta ===================================== @@ -0,0 +1,40 @@ +>NM_000546.3 Homo sapiens tumor protein p53 (TP53), mRNA +ACTTGTCATGGCGACTGTCCAGCTTTGTGCCAGGAGCCTCGCAGGGGTTGATGGGATTGGGGTTTTCCCC +TCCCATGTGCTCAAGACTGGCGCTAAAAGTTTTGAGCTTCTCAAAAGTCTAGAGCCACCGTCCAGGGAGC +AGGTAGCTGCTGGGCTCCGGGGACACTTTGCGTTCGGGCTGGGAGCGTGCTTTCCACGACGGTGACACGC +TTCCCTGGATTGGCAGCCAGACTGCCTTCCGGGTCACTGCCATGGAGGAGCCGCAGTCAGATCCTAGCGT +CGAGCCCCCTCTGAGTCAGGAAACATTTTCAGACCTATGGAAACTACTTCCTGAAAACAACGTTCTGTCC +CCCTTGCCGTCCCAAGCAATGGATGATTTGATGCTGTCCCCGGACGATATTGAACAATGGTTCACTGAAG +ACCCAGGTCCAGATGAAGCTCCCAGAATGCCAGAGGCTGCTCCCCCCGTGGCCCCTGCACCAGCAGCTCC +TACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAGAAAACCTAC +CAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACGTACT +CCCCTGCCCTCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCAC +ACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTG +AGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGATGGTCTGGCCCCTCCTCAGCATCTTATCCGAG +TGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCGACATAGTGTGGTGGTGCCCTA +TGAGCCGCCTGAGGTTGGCTCTGACTGTACCACCATCCACTACAACTACATGTGTAACAGTTCCTGCATG +GGCGGCATGAACCGGAGGCCCATCCTCACCATCATCACACTGGAAGACTCCAGTGGTAATCTACTGGGAC +GGAACAGCTTTGAGGTGCGTGTTTGTGCCTGTCCTGGGAGAGACCGGCGCACAGAGGAAGAGAATCTCCG +CAAGAAAGGGGAGCCTCACCACGAGCTGCCCCCAGGGAGCACTAAGCGAGCACTGCCCAACAACACCAGC +TCCTCTCCCCAGCCAAAGAAGAAACCACTGGATGGAGAATATTTCACCCTTCAGATCCGTGGGCGTGAGC +GCTTCGAGATGTTCCGAGAGCTGAATGAGGCCTTGGAACTCAAGGATGCCCAGGCTGGGAAGGAGCCAGG +GGGGAGCAGGGCTCACTCCAGCCACCTGAAGTCCAAAAAGGGTCAGTCTACCTCCCGCCATAAAAAACTC +ATGTTCAAGACAGAAGGGCCTGACTCAGACTGACATTCTCCACTTCTTGTTCCCCACTGACAGCCTCCCA +CCCCCATCTCTCCCTCCCCTGCCATTTTGGGTTTTGGGTCTTTGAACCCTTGCTTGCAATAGGTGTGCGT +CAGAAGCACCCAGGACTTCCATTTGCTTTGTCCCGGGGCTCCACTGAACAAGTTGGCCTGCACTGGTGTT +TTGTTGTGGGGAGGAGGATGGGGAGTAGGACATACCAGCTTAGATTTTAAGGTTTTTACTGTGAGGGATG +TTTGGGAGATGTAAGAAATGTTCTTGCAGTTAAGGGTTAGTTTACAATCAGCCACATTCTAGGTAGGGGC +CCACTTCACCGTACTAACCAGGGAAGCTGTCCCTCACTGTTGAATTTTCTCTAACTTCAAGGCCCATATC +TGTGAAATGCTGGCATTTGCACCTACCTCACAGAGTGCATTGTGAGGGTTAATGAAATAATGTACATCTG +GCCTTGAAACCACCTTTTATTACATGGGGTCTAGAACTTGACCCCCTTGAGGGTGCTTGTTCCCTCTCCC +TGTTGGTCGGTGGGTTGGTAGTTTCTACAGTTGGGCAGCTGGTTAGGTAGAGGGAGTTGTCAAGTCTCTG +CTGGCCCAGCCAAACCCTGTCTGACAACCTCTTGGTGAACCTTAGTACCTAAAAGGAAATCTCACCCCAT +CCCACACCCTGGAGGATTTCATCTCTTGTATATGATGATCTGGATCCACCAAGACTTGTTTTATGCTCAG +GGTCAATTTCTTTTTTCTTTTTTTTTTTTTTTTTTCTTTTTCTTTGAGACTGGGTCTCGCTTTGTTGCCC +AGGCTGGAGTGGAGTGGCGTGATCTTGGCTTACTGCAGCCTTTGCCTCCCCGGCTCGAGCAGTCCTGCCT +CAGCCTCCGGAGTAGCTGGGACCACAGGTTCATGCCACCATGGCCAGCCAACTTTTGCATGTTTTGTAGA +GATGGGGTCTCACAGTGTTGCCCAGGCTGGTCTCAAACTCCTGGGCTCAGGCGATCCACCTGTCTCAGCC +TCCCAGAGTGCTGGGATTACAATTGTGAGCCACCACGTCCAGCTGGAAGGGTCAACATCTTTTACATTCT +GCAAGCACATCTGCATTTTCACCCCACCCTTCCCCTCCTTCTCCCTTTTTATATCCCATTTTTATATCGA +TCTCTTATTTTACAATAAAACTTTGCTGCCACCTGTGTGTCTGAGGGGTG + View it on GitLab: https://salsa.debian.org/med-team/pscan-tfbs/-/compare/d9856374c9aa7a7cb74673a0db9228493461b5b3...2763d0377f5dfb396ef2211e180d6658f2c8b251 -- View it on GitLab: https://salsa.debian.org/med-team/pscan-tfbs/-/compare/d9856374c9aa7a7cb74673a0db9228493461b5b3...2763d0377f5dfb396ef2211e180d6658f2c8b251 You're receiving this email because of your account on salsa.debian.org.
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