Shruti Sridhar pushed to branch master at Debian Med / dascrubber
Commits: c55bc2b2 by Shruti Sridhar at 2020-08-23T23:36:04+05:30 Add autopkgtest - - - - - ff221253 by Shruti Sridhar at 2020-08-23T23:37:12+05:30 Install docs - - - - - e5d671d4 by Shruti Sridhar at 2020-08-23T23:46:57+05:30 Update changelog - - - - - 5 changed files: - + debian/README.test - debian/changelog - debian/docs - + debian/tests/control - + debian/tests/run-unit-test Changes: ===================================== debian/README.test ===================================== @@ -0,0 +1,8 @@ +Notes on how this package can be tested. +──────────────────────────────────────── + +This package can be tested by running the provided test: + + sh run-unit-test + +in order to confirm its integrity. ===================================== debian/changelog ===================================== @@ -1,3 +1,14 @@ +dascrubber (1.1-2) UNRELEASED; urgency=medium + + [ Afif Elghraoui ] + * Remove myself from Uploaders + + [ Shruti Sridhar ] + * Add autopkgtest + * Install docs + + -- Shruti Sridhar <[email protected]> Sun, 23 Aug 2020 23:44:36 +0530 + dascrubber (1.1-1) unstable; urgency=medium * Team upload. ===================================== debian/docs ===================================== @@ -1 +1,3 @@ README.md +debian/README* +debian/tests/run-unit-test \ No newline at end of file ===================================== debian/tests/control ===================================== @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @,dazzdb, daligner +Restrictions: allow-stderr ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,43 @@ +#!/bin/bash +set -e + +pkg=dascrubber + +export LC_ALL=C.UTF-8 +if [ "${AUTOPKGTEST_TMP}" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM +fi + +#cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}" + +cd "${AUTOPKGTEST_TMP}" + +#do_stuff_to_test_package# +rangen 1.0 -r2020 >R.fasta +fasta2DAM R R.fasta +dsimulator R -c20. -r2020 >G.fasta +fasta2DB G G.fasta +rm G.fasta +DBsplit -s11 G +DBdust G.1 +DBdust G.2 +DBstats -mdust G +cat G.db + +HPC.daligner -mdust -t5 G | sh -v + +DAScover -v G G.1 G.2 +Catrack G covr +DASqv -c20 -v G G.1 G.2 +Catrack -v G qual +DAStrim -v -g20 -b20 G G.1 G.2 +Catrack -v G trim +DASpatch -v G G.1 G.2 +Catrack G patch +DASedit -v G G1 +DASmap G1 + +# Since the output is not consistent. +#It cannot be compared with the reference. + View it on GitLab: https://salsa.debian.org/med-team/dascrubber/-/compare/a0bfd5af082a14fa4e4c3442b4ef1c4f288fb48a...e5d671d44fbb6d408810086678b99a7c0be8fc07 -- View it on GitLab: https://salsa.debian.org/med-team/dascrubber/-/compare/a0bfd5af082a14fa4e4c3442b4ef1c4f288fb48a...e5d671d44fbb6d408810086678b99a7c0be8fc07 You're receiving this email because of your account on salsa.debian.org.
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