Pranav Ballaney pushed to branch master at Debian Med / seer
Commits: 21df148a by Pranav Ballaney at 2020-06-02T03:35:10+05:30 Add autopkgtests - - - - - 304f82cc by Pranav Ballaney at 2020-06-02T03:35:41+05:30 Add docs - - - - - 6 changed files: - + debian/README.test - debian/changelog - + debian/docs - debian/examples - + 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 +1,17 @@ +seer (1.1.4-3) UNRELEASED; urgency=medium + + [ Steffen Moeller ] + * d/u/metadata: yamllint + + [ Steffen Möller ] + * Update metadata with ref to conda + + [ Pranav Ballaney ] + * Add autopkgtests + * Add docs + + -- Pranav Ballaney <[email protected]> Tue, 02 Jun 2020 03:35:16 +0530 + seer (1.1.4-2) unstable; urgency=medium * debhelper 11 ===================================== debian/docs ===================================== @@ -0,0 +1,2 @@ +debian/README* +debian/tests/run-unit-test \ No newline at end of file ===================================== debian/examples ===================================== @@ -1 +1,2 @@ example_wrapper.py +test/* \ No newline at end of file ===================================== debian/tests/control ===================================== @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,60 @@ +#!/bin/bash +set -e + +pkg=seer + +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 * +gzip example_kmers +#do_stuff_to_test_package# +echo -e "\e[93m\e[1mTest 1: Basic Filters\e[0m" +seer -k example_kmers.gz -p subset.pheno +echo -e "\e[92m\e[1mPassed\e[0m" +echo + +echo -e "\e[93m\e[1mTest 2: Binary Phenotype Assocation\e[0m" +seer -k example_kmers.gz -p subset.pheno --pval 1 --chisq 1 +echo -e "\e[92m\e[1mPassed\e[0m" +echo + +echo -e "\e[93m\e[1mTest 3:Print Output\e[0m" +seer -k example_kmers.gz -p subset.pheno --pval 1 --chisq 1 --maf 0.1 --print_samples +echo -e "\e[92m\e[1mPassed\e[0m" +echo + +echo -e "\e[93m\e[1mTest 4: Continuous Phenotype Assocation\e[0m" +seer -k example_kmers.gz -p subset.cont.pheno --pval 1 --chisq 1 --maf 0.1 +echo -e "\e[92m\e[1mPassed\e[0m" +echo + +echo -e "\e[93m\e[1mTest 5: Assocation with Population Structure\e[0m" +seer -k example_kmers.gz -p example.pheno --struct all_structure_new --pval 1 --chisq 1 +echo -e "\e[92m\e[1mPassed\e[0m" +echo + +echo -e "\e[93m\e[1mTest 6: Assocation with Covariates\e[0m" +seer -k example_kmers.gz -p subset.pheno --covar_file covariates.txt --covar_list 2q,3 --pval 1 --chisq 1 +echo -e "\e[92m\e[1mPassed\e[0m" +echo + +echo -e "\e[93m\e[1mTest 7: Filter Output\e[0m" +filter_seer -k filter_in.txt --pos_beta +echo -e "\e[92m\e[1mPassed\e[0m" +echo + +echo -e "\e[93m\e[1mTest 8: Map k-mers\e[0m" +map_back -k map_in.txt -r assembly_locations.txt --threads 1 +echo -e "\e[92m\e[1mPassed\e[0m" +echo View it on GitLab: https://salsa.debian.org/med-team/seer/-/compare/46463ac8639232f5e7d97c739f57177d4448ffec...304f82cc695ae8ee30a0ba0637905389927748a1 -- View it on GitLab: https://salsa.debian.org/med-team/seer/-/compare/46463ac8639232f5e7d97c739f57177d4448ffec...304f82cc695ae8ee30a0ba0637905389927748a1 You're receiving this email because of your account on salsa.debian.org.
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