From: cbk-guest <cbk-guests@scm.alioth.debian.org>
Date: Tue, 2 Aug 2016 00:33:06 +0000 (+0300)
Subject: Autopkgtest added
X-Git-Tag: archive/raspbian/2.16.0+ds-7+rpi1~1^2~219
X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=6e9fd45573a9506640415057049e561302515736;p=ncbi-blast%2B.git

Autopkgtest added
---

diff --git a/debian/README.source b/debian/README.source
index 6dde0846..85ca5993 100644
--- a/debian/README.source
+++ b/debian/README.source
@@ -4,4 +4,6 @@ blast+ for Debian
 Lintian raises  hardening no fortify warnings that are false positives.
 
 
+Test examples taken from http://www.ncbi.nlm.nih.gov/books/NBK52640/
 
+-- Canberk Koç <canberkkoc@gmail.com> Tue, 2 Aug 2016 03:30:33 +0300
diff --git a/debian/changelog b/debian/changelog
index 6374d96a..c3be456c 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+ncbi-blast+ (2.3.0-2) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * Autopkgtest added 
+
+ -- Canberk Koç <canberkkoc@gmail.com>  Tue, 02 Aug 2016 03:32:09 +0300
+
 ncbi-blast+ (2.3.0-1) unstable; urgency=medium
 
   * New upstream version
diff --git a/debian/ncbi-blast+.examples b/debian/ncbi-blast+.examples
new file mode 100644
index 00000000..e5da4986
--- /dev/null
+++ b/debian/ncbi-blast+.examples
@@ -0,0 +1 @@
+debian/ncbi-blast+.tests/*
diff --git a/debian/ncbi-blast+.tests/test.fa b/debian/ncbi-blast+.tests/test.fa
new file mode 100644
index 00000000..6db78dd5
--- /dev/null
+++ b/debian/ncbi-blast+.tests/test.fa
@@ -0,0 +1,10 @@
+>gnl|MYDB|1 this is sequence 1
+GAATTCCCGCTACAGGGGGGGCCTGAGGCACTGCAGAAAGTGGGCCTGAGCCTCGAGGATGACGGTGCTGCAGGAACCCG
+TCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACCGAGATGCGGTTTTCCTCGCAGAACGCCTTTATGCAGAA
+GTACACTCAGAAGAAGCCTTGTTTTTACTGGCAACCTGTTATTACCGCTCAGGAAAGGCATATAAAGCATATAGACTCTT
+GAAAGGACACAGTTGTACTACACCGCAATGCAAATACCTGCTTGCAAAATGTTGTGTTGATCTCAGCAAGCTTGCAGAAG
+GGGAACAAATCTTATCTGGTGGAGTGTTTAATAAGCAGAAAAGCCATGATGATATTGTTACTGAGTTTGGTGATTCAGCT
+TGCTTTACTCTTTCATTGTTGGGACATGTATATTGCAAGACAGATCGGCTTGCCAAAGGATCAGAATGTTACCAAAAGAG
+CCTTAGTTTAAATCCTTTCCTCTGGTCTCCCTTTGAATCATTATGTGAAATAGGTGAAAAGCCAGATCCTGACCAAACAT
+TTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAAGTACCTAATCATAGTTTATCT
+CACAGACAGCCTGAGACAGTTCTTACGGAAACACCCCAGGACACAATTGAATTAAACAGATTGAATTTAGAATCTTCCAA
diff --git a/debian/ncbi-blast+.tests/testdatabase.fa b/debian/ncbi-blast+.tests/testdatabase.fa
new file mode 100644
index 00000000..844ac1db
--- /dev/null
+++ b/debian/ncbi-blast+.tests/testdatabase.fa
@@ -0,0 +1,29 @@
+>gnl1 
+GAATTCCCGCTACAGGGGGGGCCTGAGGCACTGCAGAAAGTGGGCCTGAGCCTCGAGGATGACGGTGCTGCAGGAACCCG
+TCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACCGAGATGCGGTTTTCCTCGCAGAACGCCTTTATGCAGAA
+GTACACTCAGAAGAAGCCTTGTTTTTACTGGCAACCTGTTATTACCGCTCAGGAAAGGCATATAAAGCATATAGACTCTT
+GAAAGGACACAGTTGTACTACACCGCAATGCAAATACCTGCTTGCAAAATGTTGTGTTGATCTCAGCAAGCTTGCAGAAG
+GGGAACAAATCTTATCTGGTGGAGTGTTTAATAAGCAGAAAAGCCATGATGATATTGTTACTGAGTTTGGTGATTCAGCT
+TGCTTTACTCTTTCATTGTTGGGACATGTATATTGCAAGACAGATCGGCTTGCCAAAGGATCAGAATGTTACCAAAAGAG
+CCTTAGTTTAAATCCTTTCCTCTGGTCTCCCTTTGAATCATTATGTGAAATAGGTGAAAAGCCAGATCCTGACCAAACAT
+TTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAAGTACCTAATCATAGTTTATCT
+CACAGACAGCCTGAGACAGTTCTTACGGAAACACCCCAGGACACAATTGAATTAAACAGATTGAATTTAGAATCTTCCAA
+>gnl2
+GAATTCCCGCTACAGGGGGGGCCTGAGGCACTGCAGAAAGTGGGCCTGAGCCTCGAGGATGACGGTGCTGCAGGAACCCG
+TCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACCGAGATGCGGTTTTCCTCGCAGAACGCCTTTATGCAGAA
+GTACACTCAGAAGAAGCCTTGTTTTTACTGGCAACCTGTTATTACCGCTCAGGAAAGGCATATAAAGCATATAGACTCTT
+GAAAGGACACAGTTGTACTACACCGCAATGCAAATACCTGCTTGCAAAATGTTGTGTTGATCTCAGCAAGCTTGCAGAAG
+GGGAACAAATCTTATCTGGTGGAGTGTTTAATAAGCAGAAAAGCCATGATGATATTGTTACTGAGTTTGGTGATTCAGCT
+TGCTTTACTCTTTCATTGTTGGGACATGTATATTGCAAGACAGATCGGCTTGCCAAAGGATCAGAATGTTACCAAAAGAG
+CCTTAGTTTAAATCCTTTCCTCTGGTCTCCCTTTGAATCATTATGTGAAATAGGTGAAAAGCCAGATCCTGACCAAACAT
+TTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAAGTACCTAATCATAGTTTATCT
+CACAGACAGCCTGAGACAGTTCTTACGGAAACACCCCAGGACACAATTGAATTAAACAGATTGAATTTAGAATCTTCCAA
+>gnl3
+GAATTCCCGCTACAGGGGGGGCCTGAGGCACTGCAGAAAGTGGGCCTGAGCCTCGAGGATGACGGTGCTGCAGGAACCCG
+TCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACCGAGATGCGGTTTTCCTCGCAGAACGCCTTTATGCAGAA
+GTACACTCAGAAGAAGCCTTGTTTTTACTGGCAACCTGTTATTACCGCTCAGGAAAGGCATATAAAGCATATAGACTCTT
+GAAAGGACACAGTTGTACTACACCGCAATGCAAATACCTGCTTGCAAAATGTTGTGTTGATCTCAGCAAGCTTGCAGAAG
+GGGAACAAATCTTATCTGGTGGAGTGTTTAATAAGCAGAAAAGCCATGATGATATTGTTACTGAGTTTGGTGATTCAGCT
+TGCTTTACTCTTTCATTGTTGGGACATGTATATTGCAAGACAGATCGGCTTGCCAAAGGATCAGAATGTTACCAAAAGAG
+CCTTAGTTTAAATCCTTTCCTCTGGTCTCCCTTTGAATCATTATGTGAAATAGGTGAAAAGCCAGATCCTGACCAAACAT
+TTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAAGTACCTAATCATAGTTTATCT
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 00000000..d2aa55ae
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
new file mode 100644
index 00000000..7e48969b
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,24 @@
+#!/bin/bash
+set -e
+
+pkg="ncbi-blast+"
+
+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
+find . -name "*.gz" -exec gunzip \{\} \;
+
+echo '---Creating Database--'
+/usr/bin/makeblastdb -in testdatabase.fa -parse_seqids -dbtype nucl -out testdb
+echo '---Searching Database for Hits---'
+/usr/bin/blastn -query test.fa -db testdb -task blastn -dust no -outfmt "7 qseqid sseqid evalue bitscore" -max_target_seqs 2
+echo '---Search and Fetch An Entry From Database---'
+/usr/bin/blastdbcmd -db testdb -entry gnl1 -out test_query.fa
+cat test_query.fa
+
+echo "PASS"