[med-svn] [Git][med-team/vcfanno][master] 3 commits: Install directories by names to avoid confusion

[Nilesh Patra]

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 <npatra974 at gmail.com>  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
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