[med-svn] [Git][med-team/ea-utils][master] 4 commits: Add test data
Shruti Sridhar (@shruti_sridhar)
gitlab at salsa.debian.org
Wed Aug 4 13:12:27 BST 2021
Shruti Sridhar pushed to branch master at Debian Med / ea-utils
Commits:
4e7f198a by Shruti Sridhar at 2021-08-04T17:36:12+05:30
Add test data
- - - - -
1b0c9fb5 by Shruti Sridhar at 2021-08-04T17:36:51+05:30
Add get-test-data script
- - - - -
1332ed8e by Shruti Sridhar at 2021-08-04T17:37:35+05:30
Add autopkgtests
- - - - -
bad9f826 by Shruti Sridhar at 2021-08-04T17:37:58+05:30
Install docs
- - - - -
10 changed files:
- + debian/README.test
- debian/copyright
- + debian/docs
- + debian/examples
- + debian/source/include-binaries
- + debian/tests/control
- + debian/tests/data/adapters.fa
- + debian/tests/data/data.fastq.gz
- + debian/tests/get-test-data
- + debian/tests/run-unit-test
Changes:
=====================================
debian/README.test
=====================================
@@ -0,0 +1,15 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+ sh run-unit-test
+
+in order to confirm its integrity.
+────────────────────────────────────────
+Files: debian/tests/data/*
+Source: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?exp=SRX11266476&cmd=search&m=downloads&s=seq
+
+First 100 lines of the fastq file have been taken for the test and the file adapter.fa was written for testing this package.
+
+
=====================================
debian/copyright
=====================================
@@ -14,6 +14,10 @@ Copyright: © 2011 Erik Aronesty <erik at q32.com>
2010 Illumina, Inc
License: MIT
+Files: debian/tests/data/*
+Copyright: NCBI
+License: PD
+
Files: razf.c
Copyright: 2008, Jue Ruan <ruanjue at gmail.com>, Heng Li <lh3 at sanger.ac.uk>
License: BSD-2-clause
@@ -78,3 +82,24 @@ License: MIT
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
+
+License: PD
+ PUBLIC DOMAIN NOTICE
+ National Center for Biotechnology Information
+ .
+ This software/database is a "United States Government Work" under the
+ terms of the United States Copyright Act. It was written as part of
+ the author's official duties as a United States Government employee and
+ thus cannot be copyrighted. This software/database is freely available
+ to the public for use. The National Library of Medicine and the U.S.
+ Government have not placed any restriction on its use or reproduction.
+ .
+ Although all reasonable efforts have been taken to ensure the accuracy
+ and reliability of the software and data, the NLM and the U.S.
+ Government do not and cannot warrant the performance or results that
+ may be obtained by using this software or data. The NLM and the U.S.
+ Government disclaim all warranties, express or implied, including
+ warranties of performance, merchantability or fitness for any particular
+ purpose.
+ .
+ Please cite the author in any work or product based on this material.
=====================================
debian/docs
=====================================
@@ -0,0 +1,3 @@
+debian/README*
+debian/tests/run-unit-test
+debian/tests/get-test-data
=====================================
debian/examples
=====================================
@@ -0,0 +1 @@
+debian/tests/data/*
\ No newline at end of file
=====================================
debian/source/include-binaries
=====================================
@@ -0,0 +1 @@
+debian/tests/data/data.fastq.gz
\ No newline at end of file
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
=====================================
debian/tests/data/adapters.fa
=====================================
@@ -0,0 +1,2 @@
+>adapters
+ATGCTACGCATCGACTACGAC
\ No newline at end of file
=====================================
debian/tests/data/data.fastq.gz
=====================================
Binary files /dev/null and b/debian/tests/data/data.fastq.gz differ
=====================================
debian/tests/get-test-data
=====================================
@@ -0,0 +1,26 @@
+#!/bin/bash
+
+#Needs fastq-dump from the SRA toolkit to directly get the 100 raw fastq reads
+
+fastq-dump -X 100 -Z SRR14953521 | head -n100 > data.fastq
+
+mkdir -p data
+
+if [ -f data/data.fastq.gz ]
+then
+gunzip data/data.fastq.gz
+diff -u data.fastq data/data.fastq
+
+if [ `echo $?` -ne 0 ]
+then
+ echo "The data has changed, injecting new data, please check manually before upload"
+else
+ echo "The data is same, no changes needed"
+fi
+fi
+
+gzip data.fastq
+rm data/data.fastq
+mv data.fastq.gz data/data.fastq.gz
+
+echo "Done"
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,20 @@
+#!/bin/bash
+set -e
+
+pkg=ea-utils
+
+export LC_ALL=C.UTF-8
+if [ "${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}"
+
+
+fastq-mcf adapters.fa data.fastq.gz > output
+fastq-stats data.fastq.gz > statistics
+[ -s "output" ] && [ -s "statistics" ] || exit 1 && echo "PASS tests"
+
View it on GitLab: https://salsa.debian.org/med-team/ea-utils/-/compare/6d0022757c1489c8eeb0f40e0d08188b1f462cb7...bad9f826a1f76e0112fe9512c1d4c876e2874528
--
View it on GitLab: https://salsa.debian.org/med-team/ea-utils/-/compare/6d0022757c1489c8eeb0f40e0d08188b1f462cb7...bad9f826a1f76e0112fe9512c1d4c876e2874528
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