[med-svn] [Git][med-team/rockhopper][master] 10 commits: Add example data as multi-orig tarball

Mohd Bilal (@rmb) gitlab at salsa.debian.org
Thu Jul 14 14:06:21 BST 2022 


Mohd  Bilal pushed to branch master at Debian Med / rockhopper


Commits:
0cfd21bf by Mohammed Bilal at 2022-07-14T12:25:35+00:00
Add example data as multi-orig tarball

- - - - -
fc0671d7 by Mohammed Bilal at 2022-07-14T12:26:31+00:00
New upstream version 2.0.3+dfsg2
- - - - -
16c10371 by Mohammed Bilal at 2022-07-14T12:26:50+00:00
Update upstream source from tag 'upstream/2.0.3+dfsg2'

Update to upstream version '2.0.3+dfsg2'
with Debian dir fd235a2cdf3440902782fc9ad46b12cd7a134108
- - - - -
5df01f6d by Mohammed Bilal at 2022-07-14T18:14:27+05:30
Add autopkgtests

- - - - -
3dbc7582 by Mohammed Bilal at 2022-07-14T18:22:10+05:30
Add script to fetch test data

- - - - -
95a3b141 by Mohammed Bilal at 2022-07-14T18:24:44+05:30
Add copyright for test data

- - - - -
310fc555 by Mohammed Bilal at 2022-07-14T12:56:22+00:00
routine-update: Packaging update

- - - - -
55c329f4 by Mohammed Bilal at 2022-07-14T12:56:27+00:00
routine-update: Standards-Version: 4.6.1

- - - - -
7042230f by Mohammed Bilal at 2022-07-14T12:57:11+00:00
routine-update: Ready to upload to unstable

- - - - -
a26f6963 by Mohammed Bilal at 2022-07-14T12:58:53+00:00
Update changelog

- - - - -


11 changed files:

- + debian-tests-data/Example_Condition1.fastq.gz
- + debian-tests-data/Example_Condition2.fastq.gz
- + debian-tests-data/Example_denovo.fastq.gz
- debian/changelog
- debian/control
- debian/copyright
- + debian/gbp.conf
- + debian/tests/README
- + debian/tests/control
- + debian/tests/get-test-data
- + debian/tests/run-unit-test


Changes:

=====================================
debian-tests-data/Example_Condition1.fastq.gz
=====================================
Binary files /dev/null and b/debian-tests-data/Example_Condition1.fastq.gz differ


=====================================
debian-tests-data/Example_Condition2.fastq.gz
=====================================
Binary files /dev/null and b/debian-tests-data/Example_Condition2.fastq.gz differ


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


=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+rockhopper (2.0.3+dfsg2-3) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * Add example data as multi-orig tarball
+  * New upstream version 2.0.3+dfsg2
+  * Add autopkgtests
+  * Add script to fetch test data
+  * routine-update: Packaging update
+  * routine-update: Standards-Version: 4.6.1
+  * routine-update: Ready to upload to unstable
+
+ -- Mohammed Bilal <mdbilal at disroot.org>  Thu, 14 Jul 2022 12:58:15 +0000
+
 rockhopper (2.0.3+dfsg2-2) unstable; urgency=medium
 
   * Source-only upload


=====================================
debian/control
=====================================
@@ -9,7 +9,7 @@ Build-Depends: debhelper-compat (= 13),
                javahelper,
                default-jdk,
                igv
-Standards-Version: 4.6.0
+Standards-Version: 4.6.1
 Vcs-Browser: https://salsa.debian.org/med-team/rockhopper
 Vcs-Git: https://salsa.debian.org/med-team/rockhopper.git
 Homepage: https://cs.wellesley.edu/~btjaden/Rockhopper/


=====================================
debian/copyright
=====================================
@@ -28,6 +28,10 @@ Files: *
 Copyright: 2013-2014 Brian Tjaden
 License: GPL-3+
 
+Files: debian-tests-data/*
+Copyright: 2013-2014 Brian Tjaden
+License: GPL-3+
+
 Files: debian/*
 Copyright: 2018 Andreas Tille <tille at debian.org>
            2022 Pierre Gruet <pgt at debian.org>


=====================================
debian/gbp.conf
=====================================
@@ -0,0 +1,4 @@
+[DEFAULT]
+pristine-tar=True
+filter=[ '.gitignore', '.travis.yml', '.git*' ]
+component=['debian-tests-data']


=====================================
debian/tests/README
=====================================
@@ -0,0 +1,6 @@
+Tests for rockhopper
+=================
+
+The data for tests has been referenced from:
+	https://cs.wellesley.edu/~btjaden/Rockhopper/user_guide.html
+


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


=====================================
debian/tests/get-test-data
=====================================
@@ -0,0 +1,8 @@
+#!/bin/bash
+wget https://cs.wellesley.edu/~btjaden/Rockhopper/download/Example_Condition1.fastq
+wget https://cs.wellesley.edu/~btjaden/Rockhopper/download/Example_Condition2.fastq
+wget https://cs.wellesley.edu/~btjaden/Rockhopper/download/Example_denovo.fastq.gz
+mkdir data && mv Example_* data/
+tarball=$(dpkg-parsechangelog --file ../changelog | awk '/^Source:/ {print $2}')_$(dpkg-parsechangelog --file ../changelog | awk '/^Version:/ {print $2}' | cut -f1 -d-).orig-debian-tests-data.tar.gz
+tar --owner=root --group=root --mode=a+rX -cvzSf $tarball  data
+echo "Now move $tarball next to the new upstream tarball and gbp import it as usual"


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,31 @@
+#!/bin/bash
+set -e
+
+pkg=rockhopper
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp debian-tests-data/* -a "${AUTOPKGTEST_TMP}/"
+
+cd "${AUTOPKGTEST_TMP}"
+
+echo "e65adc8788546540a70dac02e99bedd9  Rockhopper_Results/summary.txt" >> checksums
+echo "4540bf9083d1149d7c158cfdd6d52e26  Rockhopper_Results/transcripts.txt" >> checksums
+echo "9b130dbe2c1bab1baa97e80a3019c063  de_novo_results/summary.txt" >> checksums
+echo "2c59b3787a789187975cf519b3833f43  de_novo_results/transcripts.txt" >> checksums
+
+echo -e "\e[93m\e[1mRunning Tests\e[0m"
+
+echo "Test 1"
+rockhopper Example_Condition1.fastq.gz,Example_Condition2.fastq.gz
+
+echo "Test 2"
+rockhopper Example_denovo.fastq.gz -o de_novo_results
+
+md5sum --check checksums
+
+echo -e "\e[92m\e[1mPASS\e[0m"



View it on GitLab: https://salsa.debian.org/med-team/rockhopper/-/compare/0fc245b2f6793f9d57ecc4cf896b5da9041556c5...a26f6963675082ac8a7ba14df73dcead2351ad2c

-- 
View it on GitLab: https://salsa.debian.org/med-team/rockhopper/-/compare/0fc245b2f6793f9d57ecc4cf896b5da9041556c5...a26f6963675082ac8a7ba14df73dcead2351ad2c
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