[med-svn] [Git][med-team/tvc][master] 7 commits: Add autopkgtests

[Mohd Bilal (@rmb)]

Mohd  Bilal pushed to branch master at Debian Med / tvc


Commits:
ca557181 by Mohammed Bilal at 2022-09-05T22:43:41+05:30
Add autopkgtests

- - - - -
869efd9c by Mohammed Bilal at 2022-09-05T17:17:52+00:00
routine-update: Packaging update

- - - - -
129181bc by Mohammed Bilal at 2022-09-05T17:17:57+00:00
routine-update: Standards-Version: 4.6.1

- - - - -
1f1b495c by Mohammed Bilal at 2022-09-05T17:17:58+00:00
routine-update: debhelper-compat 13

- - - - -
421bdcb7 by Mohammed Bilal at 2022-09-05T17:18:05+00:00
routine-update: Add salsa-ci file

- - - - -
14e4c45c by Mohammed Bilal at 2022-09-05T17:19:06+00:00
Set upstream metadata fields: Bug-Database, Bug-Submit.

Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html

- - - - -
9abc9037 by Mohammed Bilal at 2022-09-05T17:21:28+00:00
Update changelog

- - - - -


6 changed files:

- debian/changelog
- debian/control
- + debian/salsa-ci.yml
- + debian/tests/control
- + debian/tests/run-unit-test
- debian/upstream/metadata


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+tvc (5.0.3+git20151221.80e144e+dfsg-5) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * Add autopkgtest
+  * Standards-Version: 4.6.1 (routine-update)
+  * debhelper-compat 13 (routine-update)
+  * Add salsa-ci file (routine-update)
+  * Set upstream metadata fields: Bug-Database, Bug-Submit.
+
+ -- Mohammed Bilal <mdbilal at disroot.org>  Mon, 05 Sep 2022 17:20:03 +0000
+
 tvc (5.0.3+git20151221.80e144e+dfsg-4) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/control
=====================================
@@ -4,14 +4,14 @@ Uploaders: Dominique Belhachemi <domibel at debian.org>,
            Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
                cmake,
                libbamtools-dev,
                libjsoncpp-dev,
                libarmadillo-dev,
                libboost-math-dev,
                libsmithwaterman-dev
-Standards-Version: 4.5.0
+Standards-Version: 4.6.1
 Vcs-Browser: https://salsa.debian.org/med-team/tvc
 Vcs-Git: https://salsa.debian.org/med-team/tvc.git
 Homepage: http://ioncommunity.thermofisher.com


=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml


=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,32 @@
+#!/bin/bash
+set -e
+
+pkg=TVC
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/${pkg}/examples/example1/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+echo -e "Running Tests"
+
+variant_caller_pipeline.py \
+    --input-bam      test.bam \
+    --reference-fasta reference.fasta \
+    --region-bed      test_merged_plain.bed \
+    --primer-trim-bed test_unmerged_detail.bed
+
+if [ -f TSVC_variants.vcf ] && \
+   [ -f small_variants.vcf ] && \
+   [ -f small_variants_filtered.vcf ]; then
+
+   echo "PASS"
+
+else
+   echo "FAIL"
+fi


=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,5 @@
+Bug-Database: https://github.com/domibel/IonTorrent-VariantCaller/issues
+Bug-Submit: https://github.com/domibel/IonTorrent-VariantCaller/issues/new
 Registry:
  - Name: OMICtools
    Entry: OMICS_29293



View it on GitLab: https://salsa.debian.org/med-team/tvc/-/compare/ab703348ee8a5d3f1cb4f6f75b1221d87150c920...9abc9037641bafb32bf980da6563397b7a62e904

-- 
View it on GitLab: https://salsa.debian.org/med-team/tvc/-/compare/ab703348ee8a5d3f1cb4f6f75b1221d87150c920...9abc9037641bafb32bf980da6563397b7a62e904
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