Pranav Ballaney pushed to branch master at Debian Med / jaligner
Commits: 36fe8b76 by Pranav Ballaney at 2020-07-03T08:12:49+05:30 Install example and reference data - - - - - a1f25fdf by Pranav Ballaney at 2020-07-03T08:16:30+05:30 Install docs - - - - - 4cce27a5 by Pranav Ballaney at 2020-07-03T08:16:36+05:30 Add autopkgtests - - - - - ead4e864 by Pranav Ballaney at 2020-07-03T08:17:02+05:30 Add Pranav Ballaney to Uploaders - - - - - 01a98951 by Pranav Ballaney at 2020-07-03T08:19:54+05:30 Include reference binary - - - - - 9 changed files: - + debian/README.test - debian/control - + debian/docs - + debian/examples - debian/source/include-binaries - + debian/tests/README.test_data - + debian/tests/control - + debian/tests/references.tar.xz - + 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/control ===================================== @@ -1,7 +1,8 @@ Source: jaligner Maintainer: Debian Med Packaging Team <[email protected]> Uploaders: Tim Booth <[email protected]>, - Michael R. Crusoe <[email protected]> + Michael R. Crusoe <[email protected]>, + Pranav Ballaney <[email protected]> Section: science Priority: optional Build-Depends: debhelper (>= 11~), ===================================== debian/docs ===================================== @@ -0,0 +1,4 @@ +README* +debian/README* +debian/tests/README* +debian/tests/run-unit-test \ No newline at end of file ===================================== debian/examples ===================================== @@ -0,0 +1,2 @@ +src/jaligner/example/sequences/* +debian/tests/reference* \ No newline at end of file ===================================== debian/source/include-binaries ===================================== @@ -7,3 +7,4 @@ debian/images/open.gif debian/images/paste.gif debian/images/print.gif debian/images/save.gif +debian/tests/references.tar.xz \ No newline at end of file ===================================== debian/tests/README.test_data ===================================== @@ -0,0 +1,3 @@ +references.tar.xz contains output files produced by running jaligner on +p53_human and p53_mouse, which come with the jaligner package. +The jaligner command is provided in run-unit-test. \ No newline at end of file ===================================== debian/tests/control ===================================== @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr ===================================== debian/tests/references.tar.xz ===================================== Binary files /dev/null and b/debian/tests/references.tar.xz differ ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,29 @@ +#!/bin/bash +set -e + +pkg=jaligner + +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 ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM +fi + +cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}" + +cd "${AUTOPKGTEST_TMP}" + +gunzip -r * +tar -xf references.tar.xz +ls -R +#do_stuff_to_test_package# +matrices=$(ls /usr/share/jaligner/jaligner/matrix/matrices) + +for matrix in $matrices; +do + jaligner p53_human.fasta p53_mouse.fasta ${matrix} 10 0.5 > result.${matrix}.txt + diff reference.${matrix}.txt result.${matrix}.txt +done View it on GitLab: https://salsa.debian.org/med-team/jaligner/-/compare/ef763cb7d2ae2ab81acf0f9d25e5516f1f098358...01a98951682a3f5f013daa2a8723b74f89b1cb45 -- View it on GitLab: https://salsa.debian.org/med-team/jaligner/-/compare/ef763cb7d2ae2ab81acf0f9d25e5516f1f098358...01a98951682a3f5f013daa2a8723b74f89b1cb45 You're receiving this email because of your account on salsa.debian.org.
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