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

Fri Jun 8 15:23:08 BST 2018

Liubov Chuprikova pushed to branch master at Debian Med / soapdenovo


Commits:
2c384317 by Liubov Chuprikova at 2018-06-08T16:09:28+02:00
Add autopkgtest

- - - - -
68f684a8 by Liubov Chuprikova at 2018-06-08T16:17:42+02:00
Point Vcs fields to salsa.debian.org

- - - - -
b96b723e by Liubov Chuprikova at 2018-06-08T16:20:16+02:00
Standards-Version: 4.1.4

- - - - -


9 changed files:

- + debian/README.test
- debian/changelog
- debian/control
- debian/copyright
- debian/docs
- + debian/source/include-binaries
- + debian/tests/control
- + debian/tests/run-unit-test
- + debian/tests/test-data/SRR7262809.fastq.tar.gz


Changes:

=====================================
debian/README.test
=====================================

--- /dev/null
+++ b/debian/README.test
@@ -0,0 +1,8 @@
+Notes on how this package can be tested.
+_______________________________________
+
+This package can be tested by execution
+
+	sh run-unit-test
+
+in order to confirm its integrity.


=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,9 +1,15 @@
 soapdenovo (1.05-5) UNRELEASED; urgency=medium
 
+  [ Steffen Moeller ]
   * debian/upstream/metadata:
     - Added references to registries.
     - yamllint clean
 
+  [ Liubov Chuprikova ]
+  * Add autopkgtest
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.1.4
+
  -- Steffen Moeller <moeller at debian.org>  Wed, 06 Sep 2017 23:50:52 +0200
 
 soapdenovo (1.05-4) unstable; urgency=medium


=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -5,9 +5,9 @@ Section: science
 Priority: optional
 Build-Depends: debhelper (>= 10),
                rename
-Standards-Version: 4.1.0
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/soapdenovo.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/soapdenovo.git
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/soapdenovo
+Vcs-Git: https://salsa.debian.org/med-team/soapdenovo.git
 Homepage: http://soap.genomics.org.cn/soapdenovo.html
 
 Package: soapdenovo


=====================================
debian/copyright
=====================================
--- a/debian/copyright
+++ b/debian/copyright
@@ -39,3 +39,21 @@ License: GPL-2+
  .
  On Debian systems, the complete text of the GNU General
  Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+Files: debian/tests/test-data/SRR7262809.fastq.tar.gz
+Copyright: 1996-2018 NCBI
+License: unrestricted
+ Databases of molecular data on the NCBI Web site include such examples as
+ nucleotide sequences (GenBank), protein sequences, macromolecular
+ structures, molecular variation, gene expression, and mapping data. They
+ are designed to provide and encourage access within the scientific
+ community to sources of current and comprehensive information. Therefore,
+ NCBI itself places no restrictions on the use or distribution of the data
+ contained therein. Nor do we accept data when the submitter has requested
+ restrictions on reuse or redistribution.
+Comment:
+ The test data files contained in the archive are a small data set prepared
+ from the original SRA with accession number SRR7262809.
+ .
+ To download the original file you can use fastq-dump tool from SRA Toolkit:
+    fastq-dump --split-3 SRR7262809


=====================================
debian/docs
=====================================
--- a/debian/docs
+++ b/debian/docs
@@ -1 +1,4 @@
 MANUAL
+debian/tests/test-data
+debian/tests/run-unit-test
+debian/README.test


=====================================
debian/source/include-binaries
=====================================
--- /dev/null
+++ b/debian/source/include-binaries
@@ -0,0 +1 @@
+debian/tests/test-data/SRR7262809.fastq.tar.gz


=====================================
debian/tests/control
=====================================
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,2 @@
+Tests: run-unit-test
+Depends: @


=====================================
debian/tests/run-unit-test
=====================================
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,44 @@
+#!/bin/sh -e
+
+pkg="soapdenovo"
+
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+    AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+    trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
+fi
+cd $AUTOPKGTEST_TMP
+cp -a /usr/share/doc/${pkg}/test-data/* .
+tar -xzvf *.tar.gz; rm *.tar.gz
+
+echo ">>>>>Starting soapdenovo test..."
+echo ">>>>>Step 1: pregraph"
+soapdenovo-31mer pregraph -s example.config -o graph
+[ -s graph.kmerFreq ]
+[ -s graph.edge ]
+[ -s graph.preArc ]
+[ -s graph.vertex ]
+[ -s graph.preGraphBasic ]
+
+echo ">>>>>Step 2: contig"
+soapdenovo-31mer contig -g graph
+[ -s graph.contig ]
+[ -s graph.Arc ]
+[ -s graph.updated.edge ]
+[ -s graph.ContigIndex ]
+
+echo ">>>>>Step 3: map"
+soapdenovo-31mer map -s example.config -g graph
+[ -s graph.peGrads ]
+[ -s graph.readOnContig ]
+[ -s graph.readInGap ]
+
+echo ">>>>>Step 4: scaff"
+soapdenovo-31mer scaff -g graph
+[ -s graph.newContigIndex ]
+[ -s graph.links ]
+[ -s graph.scaf_gap ]
+[ -s graph.scaf ]
+[ -e graph.gapSeq ]
+[ -s graph.scafSeq ]
+
+echo ""; echo "PASS"; echo ""


=====================================
debian/tests/test-data/SRR7262809.fastq.tar.gz
=====================================
Binary files /dev/null and b/debian/tests/test-data/SRR7262809.fastq.tar.gz differ



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