Pranav Ballaney pushed to branch master at Debian Med / pbdagcon
Commits: 9edbe803 by Pranav Ballaney at 2020-08-24T01:02:58+05:30 Add autopkgtests - - - - - e1512cb4 by Pranav Ballaney at 2020-08-24T01:03:04+05:30 Install docs - - - - - 46d56dc7 by Pranav Ballaney at 2020-08-24T01:03:36+05:30 Add Pranav Ballaney to Uploaders - - - - - 034d930e by Pranav Ballaney at 2020-08-24T01:03:59+05:30 Update changelog - - - - - 30a4838d by Pranav Ballaney at 2020-08-24T01:04:10+05:30 routine-update: debhelper-compat 13 - - - - - fed1eef6 by Pranav Ballaney at 2020-08-24T01:04:14+05:30 routine-update: Add salsa-ci file - - - - - e4f04611 by Pranav Ballaney at 2020-08-24T01:04:14+05:30 routine-update: Rules-Requires-Root: no - - - - - 4507c237 by Pranav Ballaney at 2020-08-24T01:05:21+05:30 routine-update: Ready to upload to unstable - - - - - 7 changed files: - + debian/README.test - debian/changelog - debian/control - debian/docs - + debian/salsa-ci.yml - + 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 @@ +pbdagcon (0.3+git20180411.c14c422+dfsg-2) unstable; urgency=medium + + * Add autopkgtests + * Install docs + * Add Pranav Ballaney to Uploaders + * debhelper-compat 13 (routine-update) + * Add salsa-ci file (routine-update) + * Rules-Requires-Root: no (routine-update) + + -- Pranav Ballaney <[email protected]> Mon, 24 Aug 2020 01:04:20 +0530 + pbdagcon (0.3+git20180411.c14c422+dfsg-1) unstable; urgency=medium * Add myself to Uploaders to have at least one human uploader after ===================================== debian/control ===================================== @@ -1,9 +1,10 @@ Source: pbdagcon Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Andreas Tille <[email protected]> +Uploaders: Andreas Tille <[email protected]>, + Pranav Ballaney <[email protected]> Section: science Priority: optional -Build-Depends: debhelper-compat (= 12), +Build-Depends: debhelper-compat (= 13), python3, zlib1g-dev, libhdf5-dev, @@ -19,6 +20,7 @@ Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/pbdagcon Vcs-Git: https://salsa.debian.org/med-team/pbdagcon.git Homepage: https://github.com/PacificBiosciences/pbdagcon +Rules-Requires-Root: no Package: pbdagcon Architecture: any ===================================== debian/docs ===================================== @@ -1 +1,3 @@ README.md +debian/README* +debian/tests/run-unit-test \ No newline at end of file ===================================== debian/salsa-ci.yml ===================================== @@ -0,0 +1,4 @@ +--- +include: + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml ===================================== debian/tests/control ===================================== @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,45 @@ +#!/bin/bash +set -e + +pkg=pbdagcon + +export LC_ALL=C.UTF-8 +if [ "${AUTOPKGTEST_TMP}" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + # Double quote below to expand the temporary directory variable now versus + # later is on purpose. + # shellcheck disable=SC2064 + trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM +fi + +cd "${AUTOPKGTEST_TMP}" + +echo -e "\e[93m\e[1mTest 1\e[0m" +rangen 0.005 -r2020 > target.fasta +fasta2DAM target target.fasta +dsimulator target -c20. -r2020 > queries.fasta +blasr queries.fasta target.fasta -m 5 --out mapped.m5 +pbdagcon mapped.m5 > consensus.fasta + +echo "6977ed74eab5a8b58c3a90e10f1cb96c consensus.fasta" >> checksums +echo "327a35213054ec8702ea35b85f3b3c44 mapped.m5" >> checksums +echo "11015d691ec4d33c7ec4d8125349b739 queries.fasta" >> checksums +echo "160c2f8c3aeb52c98403c2c1c677c13e target.dam" >> checksums +echo "63690c9bbfd08ef3ff51d040d619056a target.fasta" >> checksums + +md5sum --check checksums +echo -e "\e[92m\e[1mPassed\e[0m" + + +echo -e "\e[93m\e[1mTest 2\e[0m" +rangen 0.01 -r2020 >R.fasta +fasta2DAM R R.fasta +dsimulator R -c20. -r2020 >G.fasta +fasta2DB G G.fasta +DBsplit -s0.1 G +DBdust G.1 +DBdust G.2 +HPC.daligner -mdust -t5 G | sh -v +dazcon -ox -j 4 -s G.db -a G.1.las > corrected.fasta + +echo -e "\e[92m\e[1mPassed\e[0m" \ No newline at end of file View it on GitLab: https://salsa.debian.org/med-team/pbdagcon/-/compare/34e42f3da102b3840ce3876056d6d8fb119c6d6b...4507c237ca1676a0acb8e6e95925a9b4340518ca -- View it on GitLab: https://salsa.debian.org/med-team/pbdagcon/-/compare/34e42f3da102b3840ce3876056d6d8fb119c6d6b...4507c237ca1676a0acb8e6e95925a9b4340518ca You're receiving this email because of your account on salsa.debian.org.
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