[med-svn] [iva] 03/04: get package to almost ready state
Sascha Steinbiss
sascha-guest at moszumanska.debian.org
Mon Aug 24 22:24:03 UTC 2015
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository iva.
commit 984b297256c2022876bae0b6b1557fdf1c95c95c
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Mon Aug 24 22:19:34 2015 +0000
get package to almost ready state
---
debian/changelog | 4 ++--
debian/control | 16 +++++++-------
debian/copyright | 30 +++++++++++++++++++++------
debian/patches/remove-pypi-deps-from-setup-py | 14 ++++++++-----
debian/rules | 5 ++---
debian/watch | 3 ++-
6 files changed, 47 insertions(+), 25 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 5a8c80b..9237865 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,5 @@
-iva (0.10.1-1) UNRELEASED; urgency=low
+iva (1.0.0-1) UNRELEASED; urgency=low
* Initial release (Closes: #772547)
- -- Jorge Soares <j.s.soares at gmail.com> Tue, 18 Nov 2014 08:56:54 +0200
+ -- Sascha Steinbiss <sascha at steinbiss.name> Mon, 24 Aug 2015 21:50:35 +0000
diff --git a/debian/control b/debian/control
index 16235a5..73d5ebb 100644
--- a/debian/control
+++ b/debian/control
@@ -3,20 +3,19 @@ Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at debian.org>,
- Jorge Soares <j.s.soares at gmail.com>
+ Jorge Soares <j.s.soares at gmail.com>,
+ Sascha Steinbiss <sascha at steinbiss.name>
Build-Depends: debhelper (>= 9),
- build-essential,
libssl-dev,
bioperl,
fastaq (>= 1.6),
kmc (>= 2.0),
help2man,
mummer,
- ncbi-blast+,
python3,
- python3-setuptools,
- python3-numpy,
- python3-nose,
+ python3-setuptools,
+ python3-numpy,
+ python3-nose,
python3-networkx,
python3-pysam,
samtools,
@@ -28,8 +27,9 @@ Homepage: https://github.com/sanger-pathogens/iva
Package: iva
Architecture: any
-Depends: ${python3:Depends}
-Description: Assemble virus genomes lacking repeat sequences using Illumina read pairs
+Depends: ${misc:Depends}, ${python3:Depends}, fastaq (>= 1.6), kmc (>= 2.0), mummer, smalt, samtools
+Recommends: r-core, bioperl, trimmomatic
+Description: iterative virus assembler
IVA is a de novo assembler designed to assemble
virus genomes that have no repeat sequences,
using Illumina read pairs sequenced from mixed
diff --git a/debian/copyright b/debian/copyright
index c76e73d..2aaa229 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,11 +1,29 @@
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: <pkg>
-Source: <path_to_download>
+Upstream-Name: iva
+Source: https://github.com/sanger-pathogens/iva
Files: *
-Copyright: © 20xx-20yy <upstream>
-License: <license>
+Copyright: © 2014-2015 Martin Hunt (mh12 at sanger.ac.uk)
+License: GPL-3+
Files: debian/*
-Copyright: © 2014 maintainername <maintainer at e.mail>
-License: <license>
+Copyright: © 2015 Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+License: GPL-3+
+
+License: GPL-3+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
+
diff --git a/debian/patches/remove-pypi-deps-from-setup-py b/debian/patches/remove-pypi-deps-from-setup-py
index 782d18e..3ccc77a 100644
--- a/debian/patches/remove-pypi-deps-from-setup-py
+++ b/debian/patches/remove-pypi-deps-from-setup-py
@@ -3,11 +3,15 @@ Author: Jorge Soares <j.s.soares at gmail.com>
Last-Update: 2014-12-08
--- a/setup.py
+++ b/setup.py
-@@ -17,7 +17,5 @@
- url='https://github.com/sanger-pathogens/iva',
+@@ -42,11 +42,6 @@
scripts=glob.glob('scripts/*'),
test_suite='nose.collector',
-- install_requires=['nose >= 1.3', 'fastaq >= 1.6.0', 'networkx'],
-- dependency_links=['http://github.com/sanger-pathogens/fastaq/tarball/master#egg=fastaq-1.7.0'],
+ tests_require=['nose >= 1.3'],
+- install_requires=[
+- 'pyfastaq >= 3.0.1',
+- 'networkx >= 1.7',
+- 'pysam >= 0.8.1'
+- ],
license='GPLv3',
- )
+ classifiers=[
+ 'Development Status :: 4 - Beta',
diff --git a/debian/rules b/debian/rules
index ca23511..2e2d9bd 100755
--- a/debian/rules
+++ b/debian/rules
@@ -27,12 +27,11 @@ ratt_dir := $(CURDIR)/iva/ratt
%:
dh $@ --with python3 --buildsystem=pybuild
-
override_dh_auto_build:
chmod a-x $(read_trim_dir)/adapters.fasta
chmod a+x $(gage_dir)/getCorrectnessStats.sh
chmod a+x $(ratt_dir)/main.ratt.pl
dh_auto_build
-#override_dh_auto_test:
-#PASS
+override_dh_auto_clean:
+ rm -rf .pybuild
diff --git a/debian/watch b/debian/watch
index 922a950..71ee95c 100644
--- a/debian/watch
+++ b/debian/watch
@@ -1,2 +1,3 @@
version=3
-https://github.com/sanger-pathogens/iva/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
\ No newline at end of file
+https://github.com/sanger-pathogens/iva/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+
--
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