[med-svn] [Git][med-team/bio-rainbow][master] 12 commits: Install data for autopkgtests
Pranav Ballaney
gitlab at salsa.debian.org
Sun Aug 23 01:08:22 BST 2020
Pranav Ballaney pushed to branch master at Debian Med / bio-rainbow
Commits:
f7f6d388 by Pranav Ballaney at 2020-08-23T05:14:06+05:30
Install data for autopkgtests
- - - - -
8ca3ff30 by Pranav Ballaney at 2020-08-23T05:14:33+05:30
Add autopkgtests
- - - - -
dd7e3e90 by Pranav Ballaney at 2020-08-23T05:19:01+05:30
Install docs
- - - - -
194fc3e8 by Pranav Ballaney at 2020-08-23T05:26:29+05:30
Add Pranav Ballaney to Uploaders
- - - - -
9917fe5b by Pranav Ballaney at 2020-08-23T05:29:05+05:30
Update changelog
- - - - -
fa54a5d5 by Pranav Ballaney at 2020-08-23T05:29:58+05:30
routine-update: Standards-Version: 4.5.0
- - - - -
11cca782 by Pranav Ballaney at 2020-08-23T05:29:59+05:30
routine-update: debhelper-compat 13
- - - - -
539ec9d9 by Pranav Ballaney at 2020-08-23T05:30:00+05:30
routine-update: Remove trailing whitespace in debian/rules
- - - - -
2a823259 by Pranav Ballaney at 2020-08-23T05:30:00+05:30
routine-update: Add salsa-ci file
- - - - -
9f803384 by Pranav Ballaney at 2020-08-23T05:30:01+05:30
routine-update: Rules-Requires-Root: no
- - - - -
61d31d44 by Pranav Ballaney at 2020-08-23T05:31:35+05:30
Include binaries
- - - - -
aeea114a by Pranav Ballaney at 2020-08-23T05:32:57+05:30
routine-update: Ready to upload to unstable
- - - - -
13 changed files:
- + debian/README.test
- debian/changelog
- − debian/compat
- debian/control
- debian/docs
- + debian/examples
- debian/rules
- + debian/salsa-ci.yml
- + debian/source/include-binaries
- + debian/tests/control
- + debian/tests/data/R.1.fastq.gz
- + debian/tests/data/R.2.fastq.gz
- + debian/tests/run-unit-test
Changes:
=====================================
debian/README.test
=====================================
@@ -0,0 +1,18 @@
+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.
+
+Notes on the files used for testing this package.
+─────────────────────────────────────────────────
+
+R.1.fasta and R.2.fasta were generated as random
+sequences, using rangen from dazzdb and
+artfastqgenerator by running the following commands:
+
+ rangen 0.005 -r2020 > R.fasta
+ artfastqgenerator -O R -R R.fasta -S ">random"
\ No newline at end of file
=====================================
debian/changelog
=====================================
@@ -1,3 +1,22 @@
+bio-rainbow (2.0.4+dfsg-2) unstable; urgency=medium
+
+ [ Steffen Möller ]
+ * Updated bio.tools ref
+ * Added ref to conda
+
+ [ Pranav Ballaney ]
+ * Install data for autopkgtests
+ * Add autopkgtests
+ * Install docs
+ * Add Pranav Ballaney to Uploaders
+ * Standards-Version: 4.5.0 (routine-update)
+ * debhelper-compat 13 (routine-update)
+ * Remove trailing whitespace in debian/rules (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+
+ -- Pranav Ballaney <ballaneypranav at gmail.com> Sun, 23 Aug 2020 05:32:47 +0530
+
bio-rainbow (2.0.4+dfsg-1) unstable; urgency=medium
* Team upload.
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -1,14 +1,16 @@
Source: bio-rainbow
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Olivier Sallou <osallou at debian.org>
+Uploaders: Olivier Sallou <osallou at debian.org>,
+ Pranav Ballaney <ballaneypranav at gmail.com>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 13),
help2man
-Standards-Version: 4.1.4
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/bio-rainbow
Vcs-Git: https://salsa.debian.org/med-team/bio-rainbow.git
Homepage: http://sourceforge.net/projects/bio-rainbow/
+Rules-Requires-Root: no
Package: bio-rainbow
Architecture: any
=====================================
debian/docs
=====================================
@@ -1,2 +1,3 @@
-README.txt
-README.txt
+README*
+debian/README*
+debian/tests/run-unit-test
\ No newline at end of file
=====================================
debian/examples
=====================================
@@ -0,0 +1 @@
+debian/tests/data/*
\ No newline at end of file
=====================================
debian/rules
=====================================
@@ -10,7 +10,7 @@ include /usr/share/dpkg/default.mk
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
%:
- dh $@
+ dh $@
override_dh_installman:
# dh_installman is messing up .sh extension as language extension
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
debian/source/include-binaries
=====================================
@@ -0,0 +1,2 @@
+debian/tests/data/R.1.fastq.gz
+debian/tests/data/R.2.fastq.gz
\ No newline at end of file
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
=====================================
debian/tests/data/R.1.fastq.gz
=====================================
Binary files /dev/null and b/debian/tests/data/R.1.fastq.gz differ
=====================================
debian/tests/data/R.2.fastq.gz
=====================================
Binary files /dev/null and b/debian/tests/data/R.2.fastq.gz differ
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,29 @@
+#!/bin/bash
+set -e
+
+pkg=bio-rainbow
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ # Double quote below to expand the temporary directory variable now versus
+ # later is on purpose.
+ # shellcheck disable=SC2064
+ trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+gunzip -r *
+
+bio-rainbow cluster -1 R.1.fastq -2 R.2.fastq > rbcluster.out 2> log
+bio-rainbow div -i rbcluster.out -o rbdiv.out
+bio-rainbow merge -o rbasm.out -a -i rbdiv.out -N50000
+
+echo "4f0a35450f64adc3bfd6f4b664887631 rbasm.out" >> checksums
+echo "29a755de547ac393328c8b31d5f6e26d rbcluster.out" >> checksums
+echo "b7dfd0cfd2f0eade15487a72632e972d rbdiv.out" >> checksums
+
+md5sum --check checksums
\ No newline at end of file
View it on GitLab: https://salsa.debian.org/med-team/bio-rainbow/-/compare/20c752433a34bb10020f6a903a0bbe446cf5eb3a...aeea114a055c708f06d01bd398f0f122e02710ea
--
View it on GitLab: https://salsa.debian.org/med-team/bio-rainbow/-/compare/20c752433a34bb10020f6a903a0bbe446cf5eb3a...aeea114a055c708f06d01bd398f0f122e02710ea
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