[med-svn] [Git][med-team/rsem][master] Added autopkgtest

[Aikaterini Kalou]

Aikaterini Kalou pushed to branch master at Debian Med / rsem


Commits:
18c02c28 by Aikaterini Kalou at 2018-03-14T19:20:57+02:00
Added autopkgtest

- - - - -


8 changed files:

- + debian/README.test
- debian/changelog
- + debian/examples/mouse_ref_building_from_transcripts.tar.gz
- debian/rsem.docs
- + debian/rsem.examples
- + debian/source/include-binaries
- + debian/tests/control
- + debian/tests/run-unit-test


Changes:

=====================================
debian/README.test
=====================================
--- /dev/null
+++ b/debian/README.test
@@ -0,0 +1,14 @@
+Notes on how this package can be tested.
+
+
+This package can be tested by executing
+
+   sh run-unit-test
+
+in order to confirm its integrity.
+
+Note: The sample data are obtained via
+
+    wget -q https://www.dropbox.com/s/ie67okalzaw8zzj/mouse_ref_building_from_transcripts.tar.gz?dl=0 -O debian/examples/mouse_ref_building_from_transcripts.tar.gz
+
+More examples and datasets can be found at https://github.com/bli25ucb/RSEM_tutorial


=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,15 +1,19 @@
-rsem (1.3.0+dfsg-1) experimental; urgency=medium
+rsem (1.3.0+dfsg-2) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * Add autopkgtest
+
+ -- Katerina Kalou <aik.kalou at gmail.com>  Wed, 14 Mar 2018 18:32:55 +0200
+
+rsem (1.3.0+dfsg-1) UNRELEASED; urgency=medium
 
   * New upstream version
   * d/watch:
      - version=4
      - xz compression
   * remove code copy of samtools-1.3
-  * cme fix dpkg-control
-  * debhelper 11
-  * d/rules: do not parse d/changelog
 
- -- Andreas Tille <tille at debian.org>  Sun, 18 Feb 2018 20:34:37 +0100
+ -- Andreas Tille <tille at debian.org>  Fri, 09 Dec 2016 14:26:08 +0100
 
 rsem (1.2.31+dfsg-1) unstable; urgency=medium
 


=====================================
debian/examples/mouse_ref_building_from_transcripts.tar.gz
=====================================
Binary files /dev/null and b/debian/examples/mouse_ref_building_from_transcripts.tar.gz differ


=====================================
debian/rsem.docs
=====================================
--- a/debian/rsem.docs
+++ b/debian/rsem.docs
@@ -1,4 +1,7 @@
 README.md
+debian/README.test
 WHAT_IS_NEW
 cnt_file_description.txt
 model_file_description.txt
+debian/tests/run-unit-test
+


=====================================
debian/rsem.examples
=====================================
--- /dev/null
+++ b/debian/rsem.examples
@@ -0,0 +1,2 @@
+debian/examples/*
+


=====================================
debian/source/include-binaries
=====================================
--- /dev/null
+++ b/debian/source/include-binaries
@@ -0,0 +1,2 @@
+mouse_ref_building_from_transcripts.tar.gz
+


=====================================
debian/tests/control
=====================================
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,4 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
+


=====================================
debian/tests/run-unit-test
=====================================
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,21 @@
+#!/bin/bash
+set -e
+set -x
+
+pkg="rsem"
+
+
+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
+
+tar -C . -xzf *.tar.gz
+
+rsem-prepare-reference \
+		       --transcript-to-gene-map mouse_ref_mapping.txt \
+   		       mouse_ref.fa mouse_ref



View it on GitLab: https://salsa.debian.org/med-team/rsem/commit/18c02c28e5532ea89d54d4cee22af12584c4e0f3

---
View it on GitLab: https://salsa.debian.org/med-team/rsem/commit/18c02c28e5532ea89d54d4cee22af12584c4e0f3
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