Nilesh Patra pushed to branch master at Debian Med / scythe
Commits: 63e5f707 by Nilesh Patra at 2020-08-14T15:25:26+05:30 Add autopkgtests - - - - - 14f904da by Nilesh Patra at 2020-08-14T15:28:43+05:30 compat version: 13, standards version: 4.5.0 - - - - - 71e4bfb0 by Nilesh Patra at 2020-08-14T15:29:04+05:30 Add "Rules-Requires-Root:no" - - - - - 64bcf7ef by Nilesh Patra at 2020-08-14T15:34:44+05:30 Add hardening flags - - - - - 4 changed files: - debian/control - debian/rules - + debian/tests/control - + debian/tests/run-unit-test Changes: ===================================== debian/control ===================================== @@ -3,14 +3,15 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Kevin Murray <[email protected]> Section: science Priority: optional -Build-Depends: debhelper-compat (= 12), +Build-Depends: debhelper-compat (= 13), zlib1g-dev, markdown, check -Standards-Version: 4.4.1 +Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/scythe Vcs-Git: https://salsa.debian.org/med-team/scythe.git Homepage: https://github.com/vsbuffalo/scythe +Rules-Requires-Root: no Package: scythe Architecture: any ===================================== debian/rules ===================================== @@ -1,5 +1,8 @@ #!/usr/bin/make -f +include /usr/share/dpkg/buildflags.mk +export DEB_BUILD_MAINT_OPTIONS = hardening=+all + %: dh $@ ===================================== debian/tests/control ===================================== @@ -0,0 +1,4 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr + ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,33 @@ +#!/bin/bash +set -e + +pkg=scythe +CUR_DIR=`pwd` + +if [ "${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}/* -a "${AUTOPKGTEST_TMP}" +cp ${CUR_DIR}/testing/reads.fastq -a "${AUTOPKGTEST_TMP}" + +cd "${AUTOPKGTEST_TMP}" +gunzip -r * + +contam_rate=0.5 +mkdir -p scythe/results/$contam_rate +## scythe trimming - multiple priors for 40% contamination +i=1 +for prior in 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 +do + for rep in 01 02 03 04 05 06 07 08 09 10 + do + echo "Test $i" + echo "Testing with prior:$prior and rep:$rep" + scythe -n 0 -p $prior -a illumina_adapters.fa reads.fastq > scythe/results/$contam_rate/trimmed-$rep-$prior.fastq 2> /dev/null + echo "PASS" + ((i++)) + done +done + View it on GitLab: https://salsa.debian.org/med-team/scythe/-/compare/6021fa27c7fdd51974ffb6f4963be6ae2f4e5889...64bcf7ef1ea32e348e7a2e98045b96b1dfff2b18 -- View it on GitLab: https://salsa.debian.org/med-team/scythe/-/compare/6021fa27c7fdd51974ffb6f4963be6ae2f4e5889...64bcf7ef1ea32e348e7a2e98045b96b1dfff2b18 You're receiving this email because of your account on salsa.debian.org.
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