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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 ] -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/rna-star.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
