[med-svn] [rna-star] 03/04: add tests
Sascha Steinbiss
sascha at steinbiss.name
Tue May 24 09:44:45 UTC 2016
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository rna-star.
commit 3a229520835de20cdf271df0440c900a7492b7c4
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Tue May 24 09:24:57 2016 +0000
add tests
---
debian/changelog | 2 +-
debian/control | 1 +
debian/rules | 3 +++
debian/source/include-binaries | 2 ++
debian/tests/README.test | 4 ++++
debian/tests/control | 3 +++
debian/tests/foo.fa.gz | Bin 0 -> 31735 bytes
debian/tests/foo.gtf | 48 +++++++++++++++++++++++++++++++++++++++++
debian/tests/reads.fastq.gz | Bin 0 -> 334086 bytes
debian/tests/run_test.sh | 20 +++++++++++++++++
10 files changed, 82 insertions(+), 1 deletion(-)
diff --git a/debian/changelog b/debian/changelog
index a422263..0c6b340 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,8 @@
rna-star (2.5.2a+dfsg-3) unstable; urgency=medium
* Limit architectures to amd64 as supported by upstream.
- - Closes: #824997
* Add myself to Uploaders.
+ * Add tests (autopkgtest and build time)
-- Sascha Steinbiss <sascha at steinbiss.name> Sun, 22 May 2016 12:34:12 +0000
diff --git a/debian/control b/debian/control
index 3668a3a..1b0ecd5 100644
--- a/debian/control
+++ b/debian/control
@@ -10,6 +10,7 @@ Build-Depends: debhelper (>= 9),
vim-common,
zlib1g-dev
Standards-Version: 3.9.8
+Testsuite: autopkgtest
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/rna-star.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/rna-star.git
Homepage: https://github.com/alexdobin/STAR/
diff --git a/debian/rules b/debian/rules
index 1e0da99..556fe37 100755
--- a/debian/rules
+++ b/debian/rules
@@ -23,3 +23,6 @@ override_dh_auto_clean:
override_dh_compress:
dh_compress --exclude=.pdf
+
+override_dh_auto_test:
+ debian/tests/run_test.sh $(CURDIR)/source/STAR
diff --git a/debian/source/include-binaries b/debian/source/include-binaries
new file mode 100644
index 0000000..9093cff
--- /dev/null
+++ b/debian/source/include-binaries
@@ -0,0 +1,2 @@
+debian/tests/foo.fa.gz
+debian/tests/reads.fastq.gz
diff --git a/debian/tests/README.test b/debian/tests/README.test
new file mode 100644
index 0000000..2013a35
--- /dev/null
+++ b/debian/tests/README.test
@@ -0,0 +1,4 @@
+The sequence in this directory has been randomly generated for testing purposes only using GenomeTools.
+Reads have been simulated using Flux Simulator 1.2.1 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488205/).
+
+Sascha Steinbiss <sascha at steinbiss.name> 24/5/2016
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 0000000..5aa538c
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,3 @@
+Test-Command: debian/tests/run_test.sh STAR
+Depends: @
+
diff --git a/debian/tests/foo.fa.gz b/debian/tests/foo.fa.gz
new file mode 100644
index 0000000..51c96ff
Binary files /dev/null and b/debian/tests/foo.fa.gz differ
diff --git a/debian/tests/foo.gtf b/debian/tests/foo.gtf
new file mode 100644
index 0000000..27c04e7
--- /dev/null
+++ b/debian/tests/foo.gtf
@@ -0,0 +1,48 @@
+foo example start_codon 335 337 0.000000 + . gene_id "FOO069W"; transcript_id "FOO069W";
+foo example CDS 335 646 0.000000 + 0 gene_id "FOO069W"; transcript_id "FOO069W";
+foo example exon 335 649 0.000000 + . gene_id "FOO069W"; transcript_id "FOO069W";
+foo example stop_codon 647 649 0.000000 + . gene_id "FOO069W"; transcript_id "FOO069W";
+foo example start_codon 538 540 0.000000 + . gene_id "FOO068W-A"; transcript_id "FOO068W-A";
+foo example CDS 538 789 0.000000 + 0 gene_id "FOO068W-A"; transcript_id "FOO068W-A";
+foo example exon 538 792 0.000000 + . gene_id "FOO068W-A"; transcript_id "FOO068W-A";
+foo example stop_codon 790 792 0.000000 + . gene_id "FOO068W-A"; transcript_id "FOO068W-A";
+foo example start_codon 2480 2482 0.000000 + . gene_id "FOO067W-A"; transcript_id "FOO067W-A";
+foo example CDS 2480 2704 0.000000 + 0 gene_id "FOO067W-A"; transcript_id "FOO067W-A";
+foo example exon 2480 2707 0.000000 + . gene_id "FOO067W-A"; transcript_id "FOO067W-A";
+foo example stop_codon 2705 2707 0.000000 + . gene_id "FOO067W-A"; transcript_id "FOO067W-A";
+foo example start_codon 10092 10094 0.000000 + . gene_id "FOO066W"; transcript_id "FOO066W";
+foo example CDS 10092 10397 0.000000 + 0 gene_id "FOO066W"; transcript_id "FOO066W";
+foo example exon 10092 10400 0.000000 + . gene_id "FOO066W"; transcript_id "FOO066W";
+foo example stop_codon 10398 10400 0.000000 + . gene_id "FOO066W"; transcript_id "FOO066W";
+foo example start_codon 12047 12049 0.000000 + . gene_id "FOO064W-B"; transcript_id "FOO064W-B";
+foo example CDS 12047 12424 0.000000 + 0 gene_id "FOO064W-B"; transcript_id "FOO064W-B";
+foo example exon 12047 12427 0.000000 + . gene_id "FOO064W-B"; transcript_id "FOO064W-B";
+foo example stop_codon 12425 12427 0.000000 + . gene_id "FOO064W-B"; transcript_id "FOO064W-B";
+foo example start_codon 21526 21528 0.000000 + . gene_id "FOO064W"; transcript_id "FOO064W";
+foo example CDS 21526 21849 0.000000 + 0 gene_id "FOO064W"; transcript_id "FOO064W";
+foo example exon 21526 21852 0.000000 + . gene_id "FOO064W"; transcript_id "FOO064W";
+foo example stop_codon 21850 21852 0.000000 + . gene_id "FOO064W"; transcript_id "FOO064W";
+foo example start_codon 31568 31570 0.000000 + . gene_id "FOO062W"; transcript_id "FOO062W";
+foo example CDS 31568 32938 0.000000 + 0 gene_id "FOO062W"; transcript_id "FOO062W";
+foo example exon 31568 32941 0.000000 + . gene_id "FOO062W"; transcript_id "FOO062W";
+foo example stop_codon 32939 32941 0.000000 + . gene_id "FOO062W"; transcript_id "FOO062W";
+foo example start_codon 33449 33451 0.000000 + . gene_id "FOO061W"; transcript_id "FOO061W";
+foo example CDS 33449 34699 0.000000 + 0 gene_id "FOO061W"; transcript_id "FOO061W";
+foo example exon 33449 34702 0.000000 + . gene_id "FOO061W"; transcript_id "FOO061W";
+foo example stop_codon 34700 34702 0.000000 + . gene_id "FOO061W"; transcript_id "FOO061W";
+foo example start_codon 35156 35158 0.000000 + . gene_id "FOO060W"; transcript_id "FOO060W";
+foo example CDS 35156 36301 0.000000 + 0 gene_id "FOO060W"; transcript_id "FOO060W";
+foo example exon 35156 36304 0.000000 + . gene_id "FOO060W"; transcript_id "FOO060W";
+foo example stop_codon 36302 36304 0.000000 + . gene_id "FOO060W"; transcript_id "FOO060W";
+foo example start_codon 36510 36512 0.000000 + . gene_id "FOO059W"; transcript_id "FOO059W";
+foo example CDS 36510 37145 0.000000 + 0 gene_id "FOO059W"; transcript_id "FOO059W";
+foo example exon 36510 37148 0.000000 + . gene_id "FOO059W"; transcript_id "FOO059W";
+foo example stop_codon 37146 37148 0.000000 + . gene_id "FOO059W"; transcript_id "FOO059W";
+foo example start_codon 37465 37467 0.000000 + . gene_id "FOO058W"; transcript_id "FOO058W";
+foo example CDS 37465 38970 0.000000 + 0 gene_id "FOO058W"; transcript_id "FOO058W";
+foo example exon 37465 38973 0.000000 + . gene_id "FOO058W"; transcript_id "FOO058W";
+foo example stop_codon 38971 38973 0.000000 + . gene_id "FOO058W"; transcript_id "FOO058W";
+foo example start_codon 39260 39262 0.000000 + . gene_id "FOO056W"; transcript_id "FOO056W";
+foo example CDS 39260 41899 0.000000 + 0 gene_id "FOO056W"; transcript_id "FOO056W";
+foo example exon 39260 41902 0.000000 + . gene_id "FOO056W"; transcript_id "FOO056W";
+foo example stop_codon 41900 41902 0.000000 + . gene_id "FOO056W"; transcript_id "FOO056W";
diff --git a/debian/tests/reads.fastq.gz b/debian/tests/reads.fastq.gz
new file mode 100644
index 0000000..5de14ff
Binary files /dev/null and b/debian/tests/reads.fastq.gz differ
diff --git a/debian/tests/run_test.sh b/debian/tests/run_test.sh
new file mode 100755
index 0000000..e57a645
--- /dev/null
+++ b/debian/tests/run_test.sh
@@ -0,0 +1,20 @@
+#!/bin/bash
+set -e
+
+ORIGDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+WORKDIR=$(mktemp -d)
+
+trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
+cd $WORKDIR
+
+zcat $ORIGDIR/foo.fa.gz > foo.fa
+$1 --runThreadN 1 --runMode genomeGenerate \
+ --genomeDir . --genomeSAindexNbases 8 \
+ --genomeFastaFiles foo.fa \
+ --sjdbGTFfile $ORIGDIR/foo.gtf
+
+zcat $ORIGDIR/reads.fastq.gz > reads.fastq
+$1 --runThreadN 1 --genomeDir . \
+ --readFilesIn reads.fastq
+
+[ -s Aligned.out.sam ]
--
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