debian/0000755000000000000000000000000012212154724007166 5ustar debian/watch0000644000000000000000000000023012212154420010203 0ustar version=3 https://pypi.python.org/packages/source/H/HTSeq/HTSeq-([0-9.p]*).tar.gz #https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p3.tar.gz debian/python-htseq.pyremove0000644000000000000000000000003312212154420013406 0ustar HTSeq.egg-info/SOURCES.txt debian/copyright0000644000000000000000000000231312212154420011111 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: HTSeq Upstream-Contact: Simon Anders Source: https://pypi.python.org/pypi/HTSeq/ License: GPL-3+ This program 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 program 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 . . On Debian systems, the full text of the GNU General Public License version 3 can be found in the file /usr/share/common-licenses/GPL-3 Files: * Copyright: 2010 Simon Anders License: GPL-3+ The full text of the license is in /usr/share/common-licenses/GPL-3 Files: debian/* Copyright: 2013 Diane Trout License: GPL-3+ The full text of the license is in /usr/share/common-licenses/GPL-3 debian/python-htseq-doc.doc-base0000644000000000000000000000057312212154420013771 0ustar Document: python-htseq Title: HTSeq: Analyzing high-throughput sequencing data with Python Author: Simon Anders Abstract: HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays. Section: Science/Biology Format: HTML Index: /usr/share/doc/python-htseq-doc/html/index.html Files: /usr/share/doc/python-htseq-doc/html/*.html debian/changelog0000644000000000000000000000077612212154420011043 0ustar htseq (0.5.4p3-2) unstable; urgency=low [ Andreas Tille ] * debian/control: - add myself to Uploaders - cme fix dpkg-control [ Diane Trout ] * build man pages in binary target and html pages in independent. * disable dh_sphinxinstall for binary build. Closes: #721780 -- Diane Trout Thu, 05 Sep 2013 10:02:53 -0700 htseq (0.5.4p3-1) unstable; urgency=low * Initial packaging (Closes: #718664) -- Diane Trout Fri, 12 Jul 2013 14:03:21 -0700 debian/python-htseq-doc.docs0000644000000000000000000000002212212154420013231 0ustar build/sphinx/html debian/source/0000755000000000000000000000000012212154420010457 5ustar debian/source/format0000644000000000000000000000001412212154420011665 0ustar 3.0 (quilt) debian/source/options0000644000000000000000000000023212212154420012072 0ustar extend-diff-ignore=HTSeq\.egg-info/.* extend-diff-ignore=HTSeq/StepVector\.py extend-diff-ignore=src/StepVector_wrap\.cxx extend-diff-ignore=src/_HTSeq\.cdebian/compat0000644000000000000000000000000212212154420010355 0ustar 9 debian/gbp.conf0000644000000000000000000000023212212154420010573 0ustar [DEFAULT] pristine-tar = True [import-orig] filter = [ 'HTSeq.egg-info/*', 'HTSeq/StepVector.py', 'src/StepVector_wrap.cxx', 'src/_HTSeq.c' ] debian/python-htseq.install0000644000000000000000000000006612212154420013214 0ustar usr/lib/python2* usr/bin/htseq-count usr/bin/htseq-qa debian/patches/0000755000000000000000000000000012212154420010606 5ustar debian/patches/add_sphinx_man_pages.patch0000644000000000000000000000120412212154420015757 0ustar Author: Diane Trout Description: Add configuration necessary to have sphinx build man pages from the provided reStructured text documentation. --- a/doc/conf.py +++ b/doc/conf.py @@ -189,7 +189,14 @@ # If false, no module index is generated. #latex_use_modindex = True - +man_pages = [ + ('qa', 'htseq-qa', + 'Perform simple quality assesment of high-throughput sequencing reads', + 'Simon Anders', '1'), + ('count', 'htseq-count', + 'Count the number of reads in a SAM alignment file that map to GFF features', + 'Simon Anders', '1'), +] html_theme_options = { "sidebarbgcolor": "#006666", debian/patches/series0000644000000000000000000000005512212154420012023 0ustar fix_version.patch add_sphinx_man_pages.patch debian/patches/fix_version.patch0000644000000000000000000000140412212154420014161 0ustar Author: Diane Trout Description: Fix missing tuple index. --- a/setup.py +++ b/setup.py @@ -9,12 +9,12 @@ sys.stderr.write( "Could not import 'setuptools', falling back to 'distutils'.\n" ) from distutils.core import setup, Extension -if sys.version_info[0] < 2 or sys.version_info < 5: +if sys.version_info < (2, 5): sys.stderr.write( "Error in setup script for HTSeq:\n" ) sys.stderr.write( "You need at least version 2.5 of Python to use HTSeq.\n" ) sys.exit( 1 ) -if sys.version_info[0] >= 3: +if sys.version_info > (3, 0, 0): sys.stderr.write( "Error in setup script for HTSeq:\n" ) sys.stderr.write( "Sorry, this package does not yet work with Python 3.\n" ) sys.stderr.write( "Please use Python 2.x, x>=5.\n" ) debian/rules0000755000000000000000000000174012212154420010241 0ustar #!/usr/bin/make -f DH_VERBOSE=1 PYTHON2=$(shell pyversions -vr) # see https://wiki.debian.org/Python/LibraryStyleGuide export http_proxy=http://127.0.9.1:9 %: dh $@ --with python2,sphinxdoc ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) test-python%: python$* setup.py test -vv override_dh_auto_test: $(PYTHON2:%=test-python%) endif override_dh_auto_build: make -C src python setup.py build # build the man pages for the binary package python setup.py build_sphinx -b man override_dh_auto_install-indep: # build the html pages for the -doc package python setup.py build_sphinx -b html override_dh_installchangelogs: dh_installchangelogs -k doc/history.rst override_dh_sphinxdoc-arch: # dh_sphinxdoc doesn't fail silently when there are no docs override_dh_auto_clean: make -C src clean rm -rf dist build MANIFEST rm -rf *.egg-info dh_auto_clean # need an explicit clean target to deal with the file named clean clean: dh $@ --with python2,sphinxdoc .PHONY: clean debian/python-htseq.manpages0000644000000000000000000000007212212154420013336 0ustar build/sphinx/man/htseq-count.1 build/sphinx/man/htseq-qa.1debian/control0000644000000000000000000000332112212154420010561 0ustar Source: htseq Maintainer: Debian Med Packaging Team Uploaders: Diane Trout , Andreas Tille Section: python Priority: optional Build-Depends: debhelper (>= 9), python-setuptools (>= 0.6b3), python-all-dev (>= 2.6.5), python-sphinx, python-numpy (>= 1:1.3.0), swig, cython (>= 0.11) Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/python-htseq.git Vcs-Git: git://anonscm.debian.org/debian-med/python-htseq.git Homepage: http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html X-Python-Version: >= 2.5 Package: python-htseq Architecture: any Depends: ${misc:Depends}, ${python:Depends}, ${shlibs:Depends} Description: high-throughput genome sequencing read analysis utilities HTSeq can be used to performing a number of common analysis tasks when working with high-throughput genome sequencing reads: . * Getting statistical summaries about the base-call quality scores to study the data quality. * Calculating a coverage vector and exporting it for visualization in a genome browser. * Reading in annotation data from a GFF file. * Assigning aligned reads from an RNA-Seq experiments to exons and genes. Package: python-htseq-doc Architecture: all Section: doc Depends: ${sphinxdoc:Depends}, ${misc:Depends} Description: documetation for HTSeq (high-throughput genome sequencing) HTSeq can be used to performing a number of common analysis tasks when working with high-throughput genome sequencing reads. . This package contains documentation in HTML form.