[med-svn] [khmer] 02/04: initial packaging

Michael Crusoe misterc-guest at moszumanska.debian.org
Fri Jan 30 21:14:11 UTC 2015 

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 <mcrusoe at msu.edu>
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 <michael.crusoe at gmail.com>  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 <michael.crusoe at gmail.com>  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 <michael.crusoe at gmail.com>  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 <michael.crusoe at gmail.com>  Thu, 25 Sep 2014 03:16:54 -0400
+
+khmer (1.2~rc1-77-g7ca05b4-1) trusty; urgency=medium
+
+  * Initial release.
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com>  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 <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Michael R. Crusoe <mcrusoe at msu.edu>
+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: khmer-project at idyll.org
+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 <michael.crusoe at gmail.com>
+
+---
+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 <michael.crusoe at gmail.com>
+
+---
+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: khmer-project at idyll.org
+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

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