[med-svn] [Git][med-team/dascrubber][master] 3 commits: Add autopkgtest

[Shruti Sridhar]

Shruti Sridhar pushed to branch master at Debian Med / dascrubber


Commits:
c55bc2b2 by Shruti Sridhar at 2020-08-23T23:36:04+05:30
Add autopkgtest

- - - - -
ff221253 by Shruti Sridhar at 2020-08-23T23:37:12+05:30
Install docs

- - - - -
e5d671d4 by Shruti Sridhar at 2020-08-23T23:46:57+05:30
Update changelog

- - - - -


5 changed files:

- + debian/README.test
- debian/changelog
- debian/docs
- + 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 +1,14 @@
+dascrubber (1.1-2) UNRELEASED; urgency=medium
+
+  [ Afif Elghraoui ]
+  * Remove myself from Uploaders
+
+  [ Shruti Sridhar ]
+  * Add autopkgtest
+  * Install docs
+
+ -- Shruti Sridhar <shruti.sridhar99 at gmail.com>  Sun, 23 Aug 2020 23:44:36 +0530
+
 dascrubber (1.1-1) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/docs
=====================================
@@ -1 +1,3 @@
 README.md
+debian/README*
+debian/tests/run-unit-test
\ No newline at end of file


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


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,43 @@
+#!/bin/bash
+set -e
+
+pkg=dascrubber
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+#cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+#do_stuff_to_test_package#
+rangen 1.0 -r2020 >R.fasta           
+fasta2DAM R R.fasta           
+dsimulator R -c20. -r2020 >G.fasta   
+fasta2DB G G.fasta            
+rm G.fasta                    
+DBsplit -s11 G                
+DBdust G.1                    
+DBdust G.2                
+DBstats -mdust G              
+cat G.db
+ 
+HPC.daligner -mdust -t5 G | sh -v
+
+DAScover -v G G.1 G.2
+Catrack G covr
+DASqv -c20 -v G G.1 G.2
+Catrack -v G qual
+DAStrim -v -g20 -b20 G G.1 G.2
+Catrack -v G trim
+DASpatch -v G G.1 G.2
+Catrack G patch
+DASedit -v G G1
+DASmap G1
+
+# Since the output is not consistent.
+#It cannot be compared with the reference. 
+



View it on GitLab: https://salsa.debian.org/med-team/dascrubber/-/compare/a0bfd5af082a14fa4e4c3442b4ef1c4f288fb48a...e5d671d44fbb6d408810086678b99a7c0be8fc07

-- 
View it on GitLab: https://salsa.debian.org/med-team/dascrubber/-/compare/a0bfd5af082a14fa4e4c3442b4ef1c4f288fb48a...e5d671d44fbb6d408810086678b99a7c0be8fc07
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