[med-svn] [Git][med-team/soapdenovo2][master] Add autopkgtest

[Liubov Chuprikova]

Liubov Chuprikova pushed to branch master at Debian Med / soapdenovo2


Commits:
ad5c6e10 by Liubov Chuprikova at 2018-06-12T18:28:44+02:00
Add autopkgtest

- - - - -


8 changed files:

- + debian/README.test
- debian/changelog
- debian/copyright
- debian/docs
- + debian/source/include-binaries
- + debian/tests/control
- + debian/tests/run-unit-test
- + debian/tests/test-data/SRR2480581.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
@@ -1,3 +1,10 @@
+soapdenovo2 (241+dfsg-3) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * Add autopkgtest
+
+ -- Liubov Chuprikova <chuprikovalv at gmail.com>  Tue, 12 Jun 2018 17:35:14 +0200
+
 soapdenovo2 (241+dfsg-2) unstable; urgency=medium
 
   * debian/upstream/metadata:


=====================================
debian/copyright
=====================================
--- a/debian/copyright
+++ b/debian/copyright
@@ -79,3 +79,21 @@ 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/SRR2480581.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 SRR2480581.
+ .
+ To download the original file you can use fastq-dump tool from SRA Toolkit:
+    fastq-dump --split-3 SRR2480581


=====================================
debian/docs
=====================================
--- a/debian/docs
+++ b/debian/docs
@@ -1 +1,4 @@
 README.md
+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/SRR2480581.fastq.tar.gz


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


=====================================
debian/tests/run-unit-test
=====================================
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,47 @@
+#!/bin/sh -e
+
+pkg="soapdenovo2"
+
+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 soapdenovo2-63mer test..."
+echo ">>>>>Step 1: pregraph"
+soapdenovo2-63mer pregraph -s example.config -o graph
+[ -s graph.kmerFreq ]
+[ -s graph.edge.gz ]
+[ -s graph.preArc ]
+[ -s graph.vertex ]
+[ -s graph.preGraphBasic ]
+
+echo ">>>>>Step 2: contig"
+soapdenovo2-63mer contig -g graph
+[ -s graph.contig ]
+[ -s graph.Arc ]
+[ -s graph.updated.edge ]
+[ -s graph.ContigIndex ]
+
+echo ">>>>>Step 3: map"
+soapdenovo2-63mer map -s example.config -g graph
+[ -s graph.peGrads ]
+[ -s graph.readOnContig.gz ]
+[ -s graph.readInGap.gz ]
+
+echo ">>>>>Step 4: scaff"
+soapdenovo2-63mer scaff -g graph
+[ -s graph.newContigIndex ]
+[ -s graph.links ]
+[ -s graph.scaf_gap ]
+[ -s graph.scaf ]
+[ -e graph.gapSeq ]
+[ -s graph.scafSeq ]
+
+# soapdenovo2-127mer testing requires lots of memory->Skipped
+
+echo ""; echo "PASS"; echo ""


=====================================
debian/tests/test-data/SRR2480581.fastq.tar.gz
=====================================
Binary files /dev/null and b/debian/tests/test-data/SRR2480581.fastq.tar.gz differ



View it on GitLab: https://salsa.debian.org/med-team/soapdenovo2/commit/ad5c6e10dd11bfe2cd51514f7c759631f5e6c99c

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