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 <sas...@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.soa...@gmail.com> Tue, 18 Nov 2014 08:56:54 +0200 + -- Sascha Steinbiss <sas...@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-packag...@lists.alioth.debian.org> Uploaders: Andreas Tille <ti...@debian.org>, - Jorge Soares <j.s.soa...@gmail.com> + Jorge Soares <j.s.soa...@gmail.com>, + Sascha Steinbiss <sas...@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 (m...@sanger.ac.uk) +License: GPL-3+ Files: debian/* -Copyright: © 2014 maintainername <maintai...@e.mail> -License: <license> +Copyright: © 2015 Debian Med Packaging Team <debian-med-packag...@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.soa...@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) + -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/iva.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit