This is an automated email from the git hooks/post-receive script. misterc-guest pushed a commit to branch master in repository khmer.
commit dc48d636770dc76acff62ff253848921346536d2 Author: Michael R. Crusoe <[email protected]> Date: Tue Jan 27 17:05:22 2015 -0500 initial packaging --- debian/changelog | 29 ++++++++++++++++++ debian/compat | 1 + debian/control | 23 ++++++++++++++ debian/copyright | 39 +++++++++++++++++++++++ debian/createmanpages | 12 ++++++++ debian/inject-into-alioth-git | 18 +++++++++++ debian/patches/local-libs | 41 +++++++++++++++++++++++++ debian/patches/older-setuptools | 36 ++++++++++++++++++++++ debian/patches/series | 2 ++ debian/rules | 7 +++++ debian/source/format | 1 + debian/upstream/metadata | 68 +++++++++++++++++++++++++++++++++++++++++ debian/watch | 34 +++++++++++++++++++++ 13 files changed, 311 insertions(+) diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..14558fb --- /dev/null +++ b/debian/changelog @@ -0,0 +1,29 @@ +khmer (1.3-1) UNRELEASED; urgency=medium + + * Update for new release + + -- Michael R. Crusoe <[email protected]> Tue, 27 Jan 2015 16:07:19 -0500 + +khmer (1.2~rc1-77-g7ca05b4-4) trusty; urgency=medium + + * Build-depends on python-nose + + -- Michael R. Crusoe <[email protected]> Thu, 25 Sep 2014 09:35:59 -0400 + +khmer (1.2~rc1-77-g7ca05b4-3) trusty; urgency=medium + + * Build-depend on zlib & bzip2 + + -- Michael R. Crusoe <[email protected]> Thu, 25 Sep 2014 03:24:43 -0400 + +khmer (1.2~rc1-77-g7ca05b4-2) trusty; urgency=medium + + * Use an older version of setuptools + + -- Michael R. Crusoe <[email protected]> Thu, 25 Sep 2014 03:16:54 -0400 + +khmer (1.2~rc1-77-g7ca05b4-1) trusty; urgency=medium + + * Initial release. + + -- Michael R. Crusoe <[email protected]> Wed, 24 Sep 2014 23:10:47 -0400 diff --git a/debian/compat b/debian/compat new file mode 100644 index 0000000..ec63514 --- /dev/null +++ b/debian/compat @@ -0,0 +1 @@ +9 diff --git a/debian/control b/debian/control new file mode 100644 index 0000000..c37c14a --- /dev/null +++ b/debian/control @@ -0,0 +1,23 @@ +Source: khmer +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Michael R. Crusoe <[email protected]> +Build-Depends: python-screed, python2.7-dev, debhelper (>= 9), dh-python, python2.7, python (>= 2.7), python | python-all | python-dev | python-all-dev, python-setuptools (>= 3.3), zlib1g-dev, libbz2-dev, python-nose +Standards-Version: 3.9.6 +Homepage: http://khmer.readthedocs.org +Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/khmer.git +Vcs-Git: http://anonscm.debian.org/gitweb/?p=debian-med/khmer.git +Testsuite: autopkgtest +X-Python-Version: 2.7 + +Package: khmer +Architecture: amd64 +Section: science +Priority: optional +Depends: python (>= 2.7), python (<< 2.8), ${misc:Depends}, ${shlibs:Depends}, ${python:Depends} +Description: In-memory DNA sequence k-mer counting, filtering & graph traversal + khmer is a library and suite of command line tools for working with DNA + sequence. It is primarily aimed at short-read sequencing data such as that + produced by the Illumina platform. khmer takes a k-mer-centric approach to + sequence analysis, hence the name. diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..3630107 --- /dev/null +++ b/debian/copyright @@ -0,0 +1,39 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: the khmer project +Upstream-Contact: [email protected] +Source: https://pypi.python.org/pypi/khmer#downloads +Files-Excluded: third-party/bzip2, third-party/zlib + +Files: * +Copyright: 2010-2015, Michigan State University +License: BSD-3-clause + Copyright (c) 2010-2015, Michigan State University. All rights reserved. + . + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions are + met: + . + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + . + * Redistributions in binary form must reproduce the above + copyright notice, this list of conditions and the following + disclaimer in the documentation and/or other materials provided + with the distribution. + . + * Neither the name of the Michigan State University nor the names + of its contributors may be used to endorse or promote products + derived from this software without specific prior written + permission. + . + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT + LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR + A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT + HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, + DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY + THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE + OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/debian/createmanpages b/debian/createmanpages new file mode 100755 index 0000000..90b2829 --- /dev/null +++ b/debian/createmanpages @@ -0,0 +1,12 @@ +#!/bin/sh +MANDIR=debian +mkdir -p $MANDIR + +VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'` + +help2man --no-info --no-discard-stderr --help-option=" " \ + --name='<optional description of the program>' \ + --version-string="$VERSION" <normalize-by-median.py> \ + > $MANDIR/<normalize-by-median.py>.1 + + diff --git a/debian/inject-into-alioth-git b/debian/inject-into-alioth-git new file mode 100755 index 0000000..02c2222 --- /dev/null +++ b/debian/inject-into-alioth-git @@ -0,0 +1,18 @@ +#!/bin/sh -e + +echo "Please verify whether this script is obsoleted by gbp-create-remote-repo !" + +# This script implements the "Git tips" given here +# http://debian-med.alioth.debian.org/docs/policy.html#git-tips +# Use it with caution since it is less testet + +DEBPKGNAME=`dpkg-parsechangelog | awk '/^Source:/ {print $2}'` +SHORTDESC=`grep "^Description: " debian/control | head -n 1 | sed 's/^Description: //'` +VCSGIT=`grep "^Vcs-Git: " debian/control | sed -e 's/^Vcs-Git: //' -e 's#git://anonscm.debian.org/#ssh://git.debian.org/git/#'` +DIRatALIOTH=`echo $VCSGIT | sed -e 's#ssh://git.debian.org/git/#/git/#' -e 's#/[^/]\+\.git##'` + +ssh git.debian.org "cd $DIRatALIOTH; ./setup-repository $DEBPKGNAME '$SHORTDESC'" +git remote add origin $VCSGIT +git push origin master +git push --all --set-upstream +git push --tags diff --git a/debian/patches/local-libs b/debian/patches/local-libs new file mode 100644 index 0000000..7a96381 --- /dev/null +++ b/debian/patches/local-libs @@ -0,0 +1,41 @@ +Description: <short summary of the patch> + TODO: Put a short summary on the line above and replace this paragraph + with a longer explanation of this change. Complete the meta-information + with other relevant fields (see below for details). To make it easier, the + information below has been extracted from the changelog. Adjust it or drop + it. + . + khmer (1.2-1) trusty; urgency=medium + . + * Initial release. +Author: Michael R. Crusoe <[email protected]> + +--- +The information above should follow the Patch Tagging Guidelines, please +checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here +are templates for supplementary fields that you might want to add: + +Origin: <vendor|upstream|other>, <url of original patch> +Bug: <url in upstream bugtracker> +Bug-Debian: http://bugs.debian.org/<bugnumber> +Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber> +Forwarded: <no|not-needed|url proving that it has been forwarded> +Reviewed-By: <name and email of someone who approved the patch> +Last-Update: <YYYY-MM-DD> + +--- khmer-1.2.orig/setup.cfg ++++ khmer-1.2/setup.cfg +@@ -8,10 +8,10 @@ attr = !known_failing,!jenkins + + [build_ext] + undef = NO_UNIQUE_RC +-# libraries = z,bz2 ++libraries = z,bz2 + ## if using system libraries +-include-dirs = lib:third-party/zlib:third-party/bzip2 +-# include-dirs = lib ++# include-dirs = lib:third-party/zlib:third-party/bzip2 ++include-dirs = lib + ## if using system libraries (broken) + + # define = NDEBUG diff --git a/debian/patches/older-setuptools b/debian/patches/older-setuptools new file mode 100644 index 0000000..3801c39 --- /dev/null +++ b/debian/patches/older-setuptools @@ -0,0 +1,36 @@ +Description: <short summary of the patch> + TODO: Put a short summary on the line above and replace this paragraph + with a longer explanation of this change. Complete the meta-information + with other relevant fields (see below for details). To make it easier, the + information below has been extracted from the changelog. Adjust it or drop + it. + . + khmer (1.2~rc1-77-g7ca05b4-1) trusty; urgency=medium + . + * Initial release. +Author: Michael R. Crusoe <[email protected]> + +--- +The information above should follow the Patch Tagging Guidelines, please +checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here +are templates for supplementary fields that you might want to add: + +Origin: <vendor|upstream|other>, <url of original patch> +Bug: <url in upstream bugtracker> +Bug-Debian: http://bugs.debian.org/<bugnumber> +Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber> +Forwarded: <no|not-needed|url proving that it has been forwarded> +Reviewed-By: <name and email of someone who approved the patch> +Last-Update: <YYYY-MM-DD> + +--- khmer-1.2~rc1-77-g7ca05b4.orig/setup.py ++++ khmer-1.2~rc1-77-g7ca05b4/setup.py +@@ -6,7 +6,7 @@ + """ Setup for khmer project. """ + + import ez_setup +-ez_setup.use_setuptools(version="3.4.1") ++ez_setup.use_setuptools(version="3.3") + + import os + import sys diff --git a/debian/patches/series b/debian/patches/series new file mode 100644 index 0000000..8a3fec5 --- /dev/null +++ b/debian/patches/series @@ -0,0 +1,2 @@ +local-libs +older-setuptools diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..e405081 --- /dev/null +++ b/debian/rules @@ -0,0 +1,7 @@ +#!/usr/bin/make -f +#export DH_VERBOSE=1 +export PYBUILD_NAME=khmer +export PYBUILD_SYSTEM=distutils + +%: + dh $@ --with python2 --buildsystem=pybuild diff --git a/debian/source/format b/debian/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/debian/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/debian/upstream/metadata b/debian/upstream/metadata new file mode 100644 index 0000000..030e434 --- /dev/null +++ b/debian/upstream/metadata @@ -0,0 +1,68 @@ +Bug-Database: https://github.com/ged-lab/khmer/issues +Bug-Submit: https://github.com/ged-lab/khmer/issues/new +Cite-As: +Changelog: https://raw.githubusercontent.com/ged-lab/khmer/master/ChangeLog +Contact: [email protected] +Funding: AFRI Competitive Grant no. 2010-65205-20361 from the USDA NIFA, National Human Genome Research Institute of the National Institutes of Health under Award Number R01HG007513 +Name: khmer +Reference: +- Author: Crusoe, Michael and Edvenson, Greg and Fish, Jordan and Howe, + Adina and McDonald, Eric and Nahum, Joshua and Nanlohy, Kaben and + Ortiz-Zuazaga, Humberto and Pell, Jason and Simpson, Jared and Scott, Camille + and Srinivasan, Ramakrishnan Rajaram and Zhang, Qingpeng and Brown, C. Titus + Title: The khmer software package: enabling efficient sequence + analysis + Publisher: Figshare + Year: 2014 + DOI: 10.6084/m9.figshare.979190 + URL: http://dx.doi.org/10.6084/m9.figshare.979190 + eprint: http://files.figshare.com/1441148/khmer_software.pdf + Type: article +- Author: Pell, Jason and Hintze, Arend and Canino-Koning, Rosangela and + Howe, Adina and Tiedje, James M. and Brown, C. Titus + title: Scaling metagenome sequence assembly with probabilistic de Bruijn + graphs + Volume: 109 + Number: 33 + Pages: 13272-13277 + Year: 2012 + DOI: 10.1073/pnas.1121464109 + Eprint: http://www.pnas.org/content/109/33/13272.full.pdf + Journal: Proceedings of the National Academy of Sciences + Type: article + URL: http://www.pnas.org/content/109/33/13272 +- Author: C. Titus Brown and Adina Howe and Qingpeng Zhang and Alexis B. + Pyrkosz and Timothy H. Brom + Title: A Reference-Free Algorithm for Computational Normalization of + Shotgun Sequencing Data + Year: 2012 + url: http://arxiv.org/abs/1203.4802 + Eprint: http://arxiv.org/pdf/1203.4802v2 +- Author: Zhang, Qingpeng AND Pell, Jason AND Canino-Koning, Rosangela + AND Howe, Adina Chuang AND Brown, C. Titus + Journal: PLoS ONE + Title: These Are Not the K-mers You Are Looking For: Efficient Online + K-mer Counting Using a Probabilistic Data Structure + Year: 2014 + Month: 07 + Volume: 9 + DOI: 10.1371/journal.pone.0101271 + Number: 7 + Type: article + Eprint: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0101271&representation=PDF +- Author: Doring, Andreas and Weese, David and Rausch, Tobias and Reinert, + Knut + Title: SeqAn An efficient, generic C++ library for sequence analysis + Journal: BMC Bioinformatics + Volume: 9 + Year: 2008 + Number: 1 + Pages: 11 + Type: article + DOI: 10.1186/1471-2105-9-11 + PMID: 18184432 + ISSN: 1471-2105 +Repository-Browse: https://github.com/ged-lab/khmer +Repository: https://github.com/ged-lab/khmer.git + + diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..403ac4b --- /dev/null +++ b/debian/watch @@ -0,0 +1,34 @@ +version=3 + +# Uncomment to examine a Webpage +# <Webpage URL> <string match> +#http://www.example.com/downloads.php #PACKAGE#-(.*)\.tar\.gz + +# Uncomment to examine a Webserver directory +#http://www.example.com/pub/#PACKAGE#-(.*)\.tar\.gz + +# Uncommment to examine a FTP server +#ftp://ftp.example.com/pub/#PACKAGE#-(.*)\.tar\.gz debian uupdate + +# Uncomment to find new files on sourceforge +# http://sf.net/#PACKAGE#/#PACKAGE#-(\d[\d\.]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz))) + +# Uncomment to find new files on GooglePages +# http://code.google.com/p/#PACKAGE#/downloads/list?can=1 \ +# .*/#PACKAGE#-([-.\d]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz))|zip) + +# Uncomment to find new files on Github +# - when using releases: +https://github.com/ged-lab/khmer/releases .*/archive/v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) +# - when using tags +# https://github.com/#GITHUBUSER#/#PACKAGE#/tags .*/#PREFIX#(\d.*)\.(?:tgz|tbz2|txz|tar\.(?:gz|bz2|xz)) +# Remark: frequently you can do s/#PREFIX#/v?/ since 'v' or nothing is quite common but there are other prefixes possible + +# if tweaking of source is needed +# \ +# debian debian/get-orig-source + +# if you need to repack and choose +dfsg prefix +# opts=dversionmangle=s/[~\+]dfsg[0-9]*// \ + +opts=repackage=+ds1 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/khmer.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
