debian/0000755000000000000000000000000012203667520007171 5ustar debian/create-manpages0000755000000000000000000000261512006754231012154 0ustar #!/bin/sh # Create manpages using help2man # When calling help2man at package build time this would require # the following Build-Depends: HELP2MANDEPENDS="help2man python-dateutil python-cogent" # Specifically the last one does not come really cheap on slow # architectures - so we build the manpages statically here missingdepends=`dpkg -l ${HELP2MANDEPENDS} | \ grep -v -e "^ii" -e "^|" -e "^++" -e "^ " -e "^..[^[:space:]]" | \ sed 's/^[a-z][a-z][[:space:]]\+\([^[:space:]]\+\)[[:space:]]\+.*/\1/'` if [ "$missingdepends" != "" ] ; then \ echo "Please install the following packages to rebuild the upstream source tarball:" echo $missingdepends exit 1 fi mandir=`dirname $0` bindir=`dirname ${mandir}`/scripts codedir=`dirname ${mandir}`/python-code version=`dpkg-parsechangelog -l${mandir}/changelog | grep Version: | cut -f2 -d' ' | cut -f1 -d- ` mkdir -p ${mandir} # later we will strip .py extension - so we need to rename the scripts here as well ln -s ${bindir}/biom_validator.py biom_validator help2man --no-info --name='Test a biom file for adherence to the format specification' \ --version-string="${version}" \ biom_validator > ${mandir}/biom_validator.1 rm biom_validator ln -s ${bindir}/convert_biom.py convert_biom PYTHONPATH=${codedir} \ help2man --no-info --name='Script to convert biom formatted files' \ convert_biom > ${mandir}/convert_biom.1 rm convert_biom debian/manpages0000644000000000000000000000001312006754426010704 0ustar debian/*.1 debian/source/0000755000000000000000000000000012002221127010453 5ustar debian/source/format0000644000000000000000000000001411301174376011677 0ustar 3.0 (quilt) debian/copyright0000644000000000000000000000266012203010222011105 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: biom-format.org Upstream-Contact: Greg Caporaso Source: http://biom-format.org/ -> links to Github download #Files-Excluded: # ._* Files: * Copyright: © 2010-2012 Greg Caporaso License: GPL Comment: The code is lacking a license statement but the WNPP bug log contains a mail from upstream http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=682199#15 confirming GPL license Files: debian/* Copyright: © 2012 Andreas Tille License: GPL License: GPL 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 2 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 package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA . On Debian systems, the full text of the GNU General Public License version 2 can be found in the file `/usr/share/common-licenses/GPL-2'. debian/upstream0000644000000000000000000000107012002222643010740 0ustar Reference: Author: Daniel McDonald and Jose C. Clemente and Justin Kuczynski and Jai R. Rideout and Jesse Stombaugh and Doug Wendel and Andreas Wilke and Susan Huse and John Hufnagle and Folker Meyer and Rob Knight and J. G. Caporaso Title: "The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome" Journal: GigaScience Year: 2012 Volume: 1 Pages: 7 DOI: 10.1186/2047-217X-1-7 URL: http://www.gigasciencejournal.com/content/1/1/7 eprint: http://www.gigasciencejournal.com/content/pdf/2047-217X-1-7.pdf debian/rules0000755000000000000000000000402412203666623010254 0ustar #!/usr/bin/make -f DH_VERBOSE := 1 pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p') version := $(shell dpkg-parsechangelog -ldebian/changelog | grep Version: | cut -f2 -d' ' | cut -f1 -d- ) bindir := $(CURDIR)/debian/$(pkg)/usr/bin mandir := $(CURDIR)/debian/$(pkg)/usr/share/man/man1 #UVER := $(shell LC_ALL=C dpkg-parsechangelog | awk '/^Version:/{print $$2;}' | sed -e 's,-[^-]*$$,,g') #CYTHONVER := $(shell dpkg -l cython | awk '/^ii/{print $$3;}' || echo 0) #MIN_CYTHONVER := 0.17~beta1-2 #NO_CYTHON := $(shell if dpkg --compare-versions $(CYTHONVER) lt $(MIN_CYTHONVER) ; then echo 0 ; else echo 1 ; fi) %: dh $@ --with python2 # ,sphinxdoc manpages: debian/create-manpages override_dh_auto_clean: dh_auto_clean find -name "._*" -exec rm -f '{}' ';' #Needed if you try to build from pristine tarball rm -rf python-code/support-code/_sparsemat.cpp override_dh_install: dh_install # remove language extension rename 's/\.py$$//;' $(bindir)/* override_dh_installman: # try to create man pages whereever possible mkdir -p $(mandir) export PYTHONPATH=$(CURDIR)/python-code ; \ help2man --no-info --version-string="$(version)" \ --name="Script to add sample and/or observation metadata to BIOM-formatted files." \ $(bindir)/add_metadata > $(mandir)/add_metadata.1 ; \ help2man --no-info --version-string="$(version)" \ --name='Test a biom file for adherence to the format specification' \ $(bindir)/biom_validator > $(mandir)/biom_validator.1 ; \ help2man --no-info --name='Script to convert biom formatted files' \ $(bindir)/convert_biom > $(mandir)/convert_biom.1 ; \ help2man --no-info --version-string="$(version)" \ --name='summarize sample or observation data in BIOM-formatted files' \ $(bindir)/print_biom_table_summary > $(mandir)/print_biom_table_summary.1 ; \ help2man --no-info --version-string="$(version)" \ --name='subset a BIOM file, over either the observations or samples' \ $(bindir)/subset_biom > $(mandir)/subset_biom.1 get-orig-source: . debian/get-orig-source debian/get-orig-source0000755000000000000000000000230512203006142012115 0ustar #!/bin/sh # Repack tarball because of ._ files set -e # Remark: A new uscan that enables easier handling of removing files can be # obtained via # git clone git://tille@git.debian.org/git/users/tille/devscripts.git # and then copy scripts/uscan.pl as uscan at the beginning of your PATH if uscan --help | grep -q -- --repack-compression ; then echo "Use new enhanced uscan" uscan --verbose --force-download --repack-compression xz exit fi NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` UNAME=`echo $NAME | sed 's/^python-//'` if ! echo $@ | grep -q upstream-version ; then VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-.\+$/\1/'` uscan --force-download else VERSION=`echo $@ | sed "s?^.*--upstream-version \([0-9.]\+\) .*${NAME}.*?\1?"` if echo "$VERSION" | grep -q "upstream-version" ; then echo "Unable to parse version number" exit fi fi TARDIR=${UNAME}-${VERSION} mkdir -p ../tarballs cd ../tarballs tar -xaf ../${TARDIR}.tgz find . -name "._*" -type f -delete GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.gz "${TARDIR}" rm -rf "${TARDIR}" debian/watch0000644000000000000000000000023712203010234010204 0ustar version=3 opts=dversionmangle=s/\+dfsg[0-9]*// \ http://biom-format.org/ ftp://thebeast.colorado.edu/pub/biom-format-releases/biom-format-([\d.]+)\.tar\.gz debian/changelog0000644000000000000000000000154212203667331011045 0ustar python-biom-format (1.1.2-1) unstable; urgency=low * debian/watch: - Enable '+dfsg' suffix in Debian versions - Fix download location - anonscm in Vcs fields * debian/control: - cme fix dpkg-control * Remove workaround cython problem which was needed when 1.0.0 was released because cython at this time was suffering from #682652 * debian/rules: - use help2man to create manpages -- Andreas Tille Thu, 15 Aug 2013 01:17:43 +0200 python-biom-format (1.0.0-1ubuntu1) precise; urgency=low * Rebuild for Precise * Minor changes to cleanup and get-orig-source that helped me -- Tim Booth Fri, 10 Aug 2012 18:08:06 +0100 python-biom-format (1.0.0-1) unstable; urgency=low * Initial release (Closes: #682242) -- Andreas Tille Fri, 03 Aug 2012 10:38:26 +0200 debian/compat0000644000000000000000000000000211757424317010377 0ustar 9 debian/control0000644000000000000000000000403412203150255010565 0ustar Source: python-biom-format Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Section: python Priority: optional Build-Depends: debhelper (>= 9), python-all-dev, python-numpy, cython (>= 0.17), help2man, python-dateutil, python-cogent Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/python-biom-format/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/python-biom-format/trunk/ Homepage: http://biom-format.org/ X-Python-Version: >= 2.6 Package: python-biom-format Architecture: any Depends: ${shlibs:Depends}, ${python:Depends}, ${misc:Depends}, python-dateutil, python-cogent Description: Biological Observation Matrix (BIOM) format The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium candidate project. . The BIOM format is designed for general use in broad areas of comparative -omics. For example, in marker-gene surveys, the primary use of this format is to represent OTU tables: the observations in this case are OTUs and the matrix contains counts corresponding to the number of times each OTU is observed in each sample. With respect to metagenome data, this format would be used to represent metagenome tables: the observations in this case might correspond to SEED subsystems, and the matrix would contain counts corresponding to the number of times each subsystem is observed in each metagenome. Similarly, with respect to genome data, this format may be used to represent a set of genomes: the observations in this case again might correspond to SEED subsystems, and the counts would correspond to the number of times each subsystem is observed in each genome.