Pranav Ballaney pushed to branch master at Debian Med / trinculo
Commits: 2a1004df by Pranav Ballaney at 2020-04-07T21:06:28+05:30 Add to maintainers - - - - - 226a5ea8 by Pranav Ballaney at 2020-04-07T21:06:41+05:30 Add autopkgtests - - - - - 2 changed files: - debian/control - debian/tests/run-unit-test Changes: ===================================== debian/control ===================================== @@ -2,7 +2,7 @@ Source: trinculo Section: science Priority: optional Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Andreas Tille <[email protected]> +Uploaders: Andreas Tille <[email protected]>, Pranav Ballaney <[email protected]> Build-Depends: debhelper-compat (= 12), liblapack-dev Standards-Version: 4.5.0 ===================================== debian/tests/run-unit-test ===================================== @@ -5,11 +5,11 @@ pkg=trinculo 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 ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM + AUTOPKGTEST_TMP=$(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/* "${AUTOPKGTEST_TMP}" @@ -17,4 +17,31 @@ cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}" cd "${AUTOPKGTEST_TMP}" #do_stuff_to_test_package# -trinculo multinom --help +echo "1. Testing frequentist association (plink)..." +trinculo multinom --bfile genotypes --pheno phenos.txt --phenoname Pheno --basepheno Control +echo "PASSED" +echo "2. Testing frequentist association (dosage)..." +trinculo multinom --dosage genotypes.dose --pheno phenos.txt --phenoname Pheno --basepheno Control +echo "PASSED" +echo "3. Testing frequentist association (covariates)..." +trinculo multinom --bfile genotypes --pheno phenos.txt --phenoname Pheno --basepheno Control --covar pcs.txt +echo "PASSED" +echo "4. Testing frequentist association (conditioning)..." +echo "SNP1" > condfile[1] +trinculo multinom --bfile genotypes --pheno phenos.txt --phenoname Pheno --basepheno Control --covar pcs.txt --condition condfile[1] +echo "PASSED" +echo "5. Testing Bayesian association..." +trinculo multinom --bfile genotypes --pheno phenos.txt --phenoname Pheno --basepheno Control --covar pcs.txt --normalize --defaultprior +echo "PASSED" +echo "6. Testing Bayesian association (prior file)..." +trinculo multinom --bfile genotypes --pheno phenos.txt --phenoname Pheno --basepheno Control --covar pcs.txt --normalize --priors priors.txt +echo "PASSED" +echo "7. Testing Bayesian model selection..." +trinculo multinom --bfile genotypes --pheno phenos.txt --phenoname Pheno --basepheno Control --covar pcs.txt --normalize --defaultprior --select +echo "PASSED" +echo "8. Testing Bayesian model selection (empirical prior)..." +trinculo multinom --bfile genotypes --pheno phenos.txt --phenoname Pheno --basepheno Control --covar pcs.txt --normalize --empiricalprior --select +echo "PASSED" +echo "9. Testing ordinal regression..." +trinculo ordinal --bfile genotypes --pheno phenos.txt --phenoname Order --covar pcs.txt +echo "PASSED" View it on GitLab: https://salsa.debian.org/med-team/trinculo/-/compare/51ae677bda3da7b75bded509c58e3642a595b714...226a5ea833ac0db3323dfc13ba0cc4ca3efa6fae -- View it on GitLab: https://salsa.debian.org/med-team/trinculo/-/compare/51ae677bda3da7b75bded509c58e3642a595b714...226a5ea833ac0db3323dfc13ba0cc4ca3efa6fae You're receiving this email because of your account on salsa.debian.org.
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