Nilesh Patra pushed to branch master at Debian Med / vcfanno
Commits: 47d53776 by Nilesh Patra at 2020-07-18T04:30:58+05:30 Install directories by names to avoid confusion - - - - - 31023108 by Nilesh Patra at 2020-07-18T04:31:12+05:30 Add autopkgtests - - - - - ecfc8be6 by Nilesh Patra at 2020-07-18T04:35:04+05:30 Add information about missing bam file - - - - - 3 changed files: - + debian/README.source - debian/tests/run-unit-test - debian/vcfanno-examples.docs Changes: ===================================== debian/README.source ===================================== @@ -0,0 +1,18 @@ +Upstream provides binary files without sources for: + +* example/ex.bam +* example/ex.bam.bai + +These have been converted to corresponding text (.sam) files with the commands: +* samtools view -h -o ex.sam example/ex.bam + +And the corresponding *.sam files are added to: debian/missing-sources + +They can be generated back with the following commands: +* cat debian/missing-sources/ex.sam| samtools view -Sb - > example/ex.bam +* samtools index data/ex.bam data/ex.bam.bai + +These commands are also being run in debian/rules since these binaries are needed for testing. + + -- Nilesh Patra <[email protected]> Sat, 18 Jul 2020 04:33:13 +0530 + ===================================== debian/tests/run-unit-test ===================================== @@ -1,7 +1,7 @@ #!/bin/bash set -e -pkg=#PACKAGENAME# +pkg=vcfanno if [ "${AUTOPKGTEST_TMP}" = "" ] ; then AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) @@ -11,8 +11,18 @@ if [ "${AUTOPKGTEST_TMP}" = "" ] ; then trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM fi -cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}" +cp -Rf /usr/share/doc/${pkg}-examples/* "${AUTOPKGTEST_TMP}" cd "${AUTOPKGTEST_TMP}" -#do_stuff_to_test_package# +vcfanno -base-path tests/data/ -lua example/custom.lua tests/data/number.conf tests/data/number-input.vcf +if [ $(grep -c "lua error in postannotation" $STDERR_FILE) != 0 ] +then + exit 1 +fi +cat $STDERR_FILE +echo "PASS" + +vcfanno tests/overwrite-multiple-alts/b/conf.toml tests/overwrite-multiple-alts/b/input.vcf +echo "PASS" + ===================================== debian/vcfanno-examples.docs ===================================== @@ -1,3 +1,4 @@ -example/* -tests/* +example +tests debian/missing-sources/* +debian/tests/run-unit-test View it on GitLab: https://salsa.debian.org/med-team/vcfanno/-/compare/dc865e05d2c0eda4bf1c13c05db275351eff657a...ecfc8be651357969c7e833349d976d1f608f06b1 -- View it on GitLab: https://salsa.debian.org/med-team/vcfanno/-/compare/dc865e05d2c0eda4bf1c13c05db275351eff657a...ecfc8be651357969c7e833349d976d1f608f06b1 You're receiving this email because of your account on salsa.debian.org.
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