[med-svn] r18638 - in trunk/packages/khmer/trunk/debian: . bin patches source upstream
Timothy Booth
tbooth-guest at moszumanska.debian.org
Fri Jan 30 17:35:23 UTC 2015
Author: tbooth-guest
Date: 2015-01-30 17:35:22 +0000 (Fri, 30 Jan 2015)
New Revision: 18638
Added:
trunk/packages/khmer/trunk/debian/bin/
trunk/packages/khmer/trunk/debian/bin/khmer
trunk/packages/khmer/trunk/debian/changelog
trunk/packages/khmer/trunk/debian/compat
trunk/packages/khmer/trunk/debian/control
trunk/packages/khmer/trunk/debian/copyright
trunk/packages/khmer/trunk/debian/createmanpages
trunk/packages/khmer/trunk/debian/inject-into-alioth-git
trunk/packages/khmer/trunk/debian/khmer-example.README.Debian
trunk/packages/khmer/trunk/debian/khmer-example.examples
trunk/packages/khmer/trunk/debian/khmer-test.install
trunk/packages/khmer/trunk/debian/khmer.1.ronn
trunk/packages/khmer/trunk/debian/khmer.docs
trunk/packages/khmer/trunk/debian/khmer.install
trunk/packages/khmer/trunk/debian/khmer.manpages
trunk/packages/khmer/trunk/debian/patches/
trunk/packages/khmer/trunk/debian/patches/disable_google_analytics
trunk/packages/khmer/trunk/debian/patches/makefile.patch
trunk/packages/khmer/trunk/debian/patches/series
trunk/packages/khmer/trunk/debian/patches/use_system_libs.patch
trunk/packages/khmer/trunk/debian/rules
trunk/packages/khmer/trunk/debian/source/
trunk/packages/khmer/trunk/debian/source/format
trunk/packages/khmer/trunk/debian/upstream/
trunk/packages/khmer/trunk/debian/upstream/metadata
trunk/packages/khmer/trunk/debian/watch
Log:
First cut at KHMER package
Added: trunk/packages/khmer/trunk/debian/bin/khmer
===================================================================
--- trunk/packages/khmer/trunk/debian/bin/khmer (rev 0)
+++ trunk/packages/khmer/trunk/debian/bin/khmer 2015-01-30 17:35:22 UTC (rev 18638)
@@ -0,0 +1,23 @@
+#!/bin/bash
+
+# Run a khmer command
+# Note silly sh-compatible way of testing if arg starts with -
+if [ "$1" = "" -o "${1#-}" != "$1" ] ; then
+ cat <<.
+Usage: khmer <script> [args]
+ khmer <script> --help
+
+Scripts available:
+.
+ls /usr/lib/khmer/bin/*.py | sed 's/.*\// /;s/\.py$//'
+exit 1
+fi
+
+
+# Set environment
+export PATH="$PATH:/usr/lib/khmer/bin"
+
+cmd=`basename "$1" .py`.py
+shift
+
+exec "/usr/lib/khmer/bin/$cmd" "$@"
Property changes on: trunk/packages/khmer/trunk/debian/bin/khmer
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/khmer/trunk/debian/changelog
===================================================================
--- trunk/packages/khmer/trunk/debian/changelog (rev 0)
+++ trunk/packages/khmer/trunk/debian/changelog 2015-01-30 17:35:22 UTC (rev 18638)
@@ -0,0 +1,13 @@
+khmer (1.1-0biolinux3) trusty; urgency=low
+
+ * Switch to 64-bit-only build as tests segfault on i386
+ * Add missing data files to -example and make the script vaguely work
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Thu, 28 Aug 2014 13:12:55 +0100
+
+khmer (1.1-0biolinux1) trusty; urgency=low
+
+ * Initial release for Bio-Linux 8
+ * Add my own khmer wrapper to run the actual scripts
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Tue, 19 Aug 2014 16:19:00 +0100
Added: trunk/packages/khmer/trunk/debian/compat
===================================================================
--- trunk/packages/khmer/trunk/debian/compat (rev 0)
+++ trunk/packages/khmer/trunk/debian/compat 2015-01-30 17:35:22 UTC (rev 18638)
@@ -0,0 +1 @@
+9
Added: trunk/packages/khmer/trunk/debian/control
===================================================================
--- trunk/packages/khmer/trunk/debian/control (rev 0)
+++ trunk/packages/khmer/trunk/debian/control 2015-01-30 17:35:22 UTC (rev 18638)
@@ -0,0 +1,57 @@
+Source: khmer
+Section: science
+Priority: optional
+Maintainer: Tim Booth <tbooth at ceh.ac.uk>
+Uploaders: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Build-Depends: debhelper (>= 9),
+ python,
+ libpython-dev,
+ zlib1g-dev,
+ libbz2-dev,
+ ruby-ronn (>= 0.7.3),
+ python-pip,
+ python-sphinx,
+ python-markupsafe,
+ python-nose,
+ python-setuptools,
+ python-screed,
+ sphinxcontrib-autoprogram
+Standards-Version: 3.9.5
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/<pkg>/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/<pkg>/trunk/
+Homepage: https://github.com/ged-lab/khmer
+
+Package: khmer
+Architecture: amd64
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}
+Description: k-mer counting, filtering and 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.
+ .
+ khmer is research software, so you should cite us when you use it in
+ scientific publications!
+ Please see the CITATION file for citation information.
+
+Package: khmer-test
+Architecture: amd64
+Depends: khmer (>= ${binary:Version}), ${misc:Depends}
+Description: k-mer counting, filtering and 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.
+ .
+ This package installs the standard test data.
+
+Package: khmer-example
+Architecture: amd64
+Depends: khmer (>= ${binary:Version}), ${misc:Depends}
+Description: k-mer counting, filtering and 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.
+ .
+ This package installs the example data used in the tutorial.
Added: trunk/packages/khmer/trunk/debian/copyright
===================================================================
--- trunk/packages/khmer/trunk/debian/copyright (rev 0)
+++ trunk/packages/khmer/trunk/debian/copyright 2015-01-30 17:35:22 UTC (rev 18638)
@@ -0,0 +1,39 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: khmer
+Source: https://github.com/ged-lab/khmer
+
+Files: *
+Copyright: © 2010-2014, Michigan State University. All rights reserved.
+License: BSD
+ 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.
+
+Files: debian/*
+Copyright: © 2014 Tim Booth <tbooth at ceh.ac.uk>
+License: MIT
Added: trunk/packages/khmer/trunk/debian/createmanpages
===================================================================
--- trunk/packages/khmer/trunk/debian/createmanpages (rev 0)
+++ trunk/packages/khmer/trunk/debian/createmanpages 2015-01-30 17:35:22 UTC (rev 18638)
@@ -0,0 +1,16 @@
+#!/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" <programname> > $MANDIR/<programname>.1
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
Property changes on: trunk/packages/khmer/trunk/debian/createmanpages
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/khmer/trunk/debian/inject-into-alioth-git
===================================================================
--- trunk/packages/khmer/trunk/debian/inject-into-alioth-git (rev 0)
+++ trunk/packages/khmer/trunk/debian/inject-into-alioth-git 2015-01-30 17:35:22 UTC (rev 18638)
@@ -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 $VCSGIT
+git push origin master
+git push --all --set-upstream
+git push --tags
Property changes on: trunk/packages/khmer/trunk/debian/inject-into-alioth-git
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/khmer/trunk/debian/khmer-example.README.Debian
===================================================================
--- trunk/packages/khmer/trunk/debian/khmer-example.README.Debian (rev 0)
+++ trunk/packages/khmer/trunk/debian/khmer-example.README.Debian 2015-01-30 17:35:22 UTC (rev 18638)
@@ -0,0 +1,10 @@
+This package contains the example data distributed with khmer.
+
+To run it:
+
+$ cp -r /usr/share/doc/khmer-example/examples ./khmer-example
+$ cd ./khmer-example/examples/stamps
+$ bash do.sh
+
+But be warned, it doesn't actually run fully and gives errors. This
+seems to be a problem with the upstream distribution.
Added: trunk/packages/khmer/trunk/debian/khmer-example.examples
===================================================================
--- trunk/packages/khmer/trunk/debian/khmer-example.examples (rev 0)
+++ trunk/packages/khmer/trunk/debian/khmer-example.examples 2015-01-30 17:35:22 UTC (rev 18638)
@@ -0,0 +1,4 @@
+examples
+sandbox
+l/*
+data
Added: trunk/packages/khmer/trunk/debian/khmer-test.install
===================================================================
--- trunk/packages/khmer/trunk/debian/khmer-test.install (rev 0)
+++ trunk/packages/khmer/trunk/debian/khmer-test.install 2015-01-30 17:35:22 UTC (rev 18638)
@@ -0,0 +1 @@
+/usr/lib/khmer/tests
Added: trunk/packages/khmer/trunk/debian/khmer.1.ronn
===================================================================
--- trunk/packages/khmer/trunk/debian/khmer.1.ronn (rev 0)
+++ trunk/packages/khmer/trunk/debian/khmer.1.ronn 2015-01-30 17:35:22 UTC (rev 18638)
@@ -0,0 +1,33 @@
+khmer(1) -- k-mer counting, filtering and graph traversal FTW!
+==========
+
+khmer is a library and toolkit for doing k-mer-based dataset analysis
+and transformations
+
+## SYNOPSIS
+
+ khmer `<prog_name>` [options] <args>
+
+eg.
+
+ khmer `load-into-counting` -x 1e8 -k 20 reads.kh reads.fa.gz
+
+## USAGE
+
+This manpage only describes the `khmer` wrapper script. To find out about
+the software and how to use it please see /usr/share/doc/khmer or else
+http://khmer.readthedocs.org/.
+
+On Debian/Ubuntu, package maintainers avoid putting large collections of scripts
+directly into the system PATH. Rather, a single wrapper script is used to launch
+the script you want to use; therefore if the khmer instructions say to run
+`load-into-counting.py ...whatever...` you need to prefix this command with
+`khmer`. Furthermore, the .py extension may be omitted, resulting in a
+command of the format shown above.
+
+If you don't like this, simply add /usr/lib/khmer/bin to your personal PATH.
+
+## AUTHOR
+
+This wrapper and manapage were written by Tim Booth, who takes no credit for
+khmer itself.
Added: trunk/packages/khmer/trunk/debian/khmer.docs
===================================================================
--- trunk/packages/khmer/trunk/debian/khmer.docs (rev 0)
+++ trunk/packages/khmer/trunk/debian/khmer.docs 2015-01-30 17:35:22 UTC (rev 18638)
@@ -0,0 +1,5 @@
+build/sphinx/html
+CITATION
+README.rst
+CONTRIBUTING.md
+TODO
Added: trunk/packages/khmer/trunk/debian/khmer.install
===================================================================
--- trunk/packages/khmer/trunk/debian/khmer.install (rev 0)
+++ trunk/packages/khmer/trunk/debian/khmer.install 2015-01-30 17:35:22 UTC (rev 18638)
@@ -0,0 +1,4 @@
+debian/bin/* /usr/bin
+#/usr/share/python
+/usr/lib/khmer/bin
+/usr/lib/python*
Added: trunk/packages/khmer/trunk/debian/khmer.manpages
===================================================================
--- trunk/packages/khmer/trunk/debian/khmer.manpages (rev 0)
+++ trunk/packages/khmer/trunk/debian/khmer.manpages 2015-01-30 17:35:22 UTC (rev 18638)
@@ -0,0 +1 @@
+debian/*.1
Added: trunk/packages/khmer/trunk/debian/patches/disable_google_analytics
===================================================================
--- trunk/packages/khmer/trunk/debian/patches/disable_google_analytics (rev 0)
+++ trunk/packages/khmer/trunk/debian/patches/disable_google_analytics 2015-01-30 17:35:22 UTC (rev 18638)
@@ -0,0 +1,32 @@
+Turn off Google analytics as per Lintian warning
+--- a/doc/conf.py
++++ b/doc/conf.py
+@@ -190,7 +190,7 @@
+ # Various settings to pass to templates:
+
+ html_context = {
+- "google_analytics_id" : 'UA-51731094-1',
++# "google_analytics_id" : 'UA-51731094-1',
+ "disqus_shortname" : 'khmer-docs',
+ # "github_base_account" : 'ged-lab',
+ "github_project" : 'khmer',
+
+--- khmer-1.1.orig/doc/_templates/page.html
++++ khmer-1.1/doc/_templates/page.html
+@@ -61,6 +61,7 @@
+
+ {% endif %}
+
++{% if google_analytics_id %}
+ <script type="text/javascript">
+
+ var _gaq = _gaq || [];
+@@ -74,6 +75,7 @@
+ })();
+
+ </script>
++{% endif %}
+
+ {% endblock %}
+
+
Added: trunk/packages/khmer/trunk/debian/patches/makefile.patch
===================================================================
--- trunk/packages/khmer/trunk/debian/patches/makefile.patch (rev 0)
+++ trunk/packages/khmer/trunk/debian/patches/makefile.patch 2015-01-30 17:35:22 UTC (rev 18638)
@@ -0,0 +1,11 @@
+--- a/Makefile
++++ b/Makefile
+@@ -9,7 +9,7 @@
+ SOURCES=$(PYSOURCES) $(CPPSOURCES) setup.py
+
+ GCOVRURL=git+https://github.com/nschum/gcovr.git@never-executed-branches
+-VERSION=$(shell git describe --tags --dirty | sed s/v//)
++#VERSION=$(shell git describe --tags --dirty | sed s/v//)
+
+ all: khmer/_khmermodule.so
+
Added: trunk/packages/khmer/trunk/debian/patches/series
===================================================================
--- trunk/packages/khmer/trunk/debian/patches/series (rev 0)
+++ trunk/packages/khmer/trunk/debian/patches/series 2015-01-30 17:35:22 UTC (rev 18638)
@@ -0,0 +1,3 @@
+use_system_libs.patch
+disable_google_analytics
+makefile.patch
Added: trunk/packages/khmer/trunk/debian/patches/use_system_libs.patch
===================================================================
--- trunk/packages/khmer/trunk/debian/patches/use_system_libs.patch (rev 0)
+++ trunk/packages/khmer/trunk/debian/patches/use_system_libs.patch 2015-01-30 17:35:22 UTC (rev 18638)
@@ -0,0 +1,34 @@
+--- a/lib/Makefile
++++ b/lib/Makefile
+@@ -168,7 +168,7 @@
+ CORE_OBJS= error.o khmer_config.o thread_id_map.o trace_logger.o perf_metrics.o kmer_hash.o
+ PARSERS_OBJS= read_parsers.o
+
+-all: $(ZLIB_OBJS) $(BZIP2_OBJS) $(CORE_OBJS) $(PARSERS_OBJS) hashtable.o hashbits.o subset.o counting.o test aligner.o scoringmatrix.o node.o kmer.o
++all: $(CORE_OBJS) $(PARSERS_OBJS) hashtable.o hashbits.o subset.o counting.o test aligner.o scoringmatrix.o node.o kmer.o
+
+ clean:
+ -(cd $(ZLIB_DIR) && make distclean)
+--- a/setup.cfg
++++ b/setup.cfg
+@@ -8,7 +8,7 @@
+
+ [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
+--- a/setup.py
++++ b/setup.py
+@@ -5,8 +5,7 @@
+ # Contact: khmer-project at idyll.org
+ """ Setup for khmer project. """
+
+-import ez_setup
+-ez_setup.use_setuptools(version="3.4.1")
++import setuptools
+
+ import os
+ import sys
Added: trunk/packages/khmer/trunk/debian/rules
===================================================================
--- trunk/packages/khmer/trunk/debian/rules (rev 0)
+++ trunk/packages/khmer/trunk/debian/rules 2015-01-30 17:35:22 UTC (rev 18638)
@@ -0,0 +1,49 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+# some helpful variables - uncomment them if needed
+# shamelessly stolen from http://jmtd.net/log/awk/
+DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
+VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
+#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
+#GIT_TAG := $(subst ~,_,$(VERSION))
+
+%:
+ dh $@ --with=python2
+
+override_dh_clean:
+ dh_clean
+ rm -rf _develop
+ rm -rf *.egg-info
+ rm -rf third-party
+ rm -rf *.zip
+ find -name '.git*' -delete
+ rm -f debian/*.1
+ rm -rf l
+
+override_dh_auto_clean:
+ dh_auto_clean
+ rm -rf build
+ find -name '*.pyc' -delete
+
+override_dh_auto_install:
+ python setup.py install --force --root=./debian/tmp --no-compile -O0 --install-layout=deb --install-scripts=/usr/lib/khmer/bin
+ mv debian/tmp/usr/lib/python*/dist-packages/khmer/tests debian/tmp/usr/lib/khmer
+
+override_dh_auto_build:
+ dh_auto_build
+ #This is awkward...
+ mkdir _develop
+ env PYTHONPATH="`pwd`/_develop" python ./setup.py develop -d _develop
+ make doc VERSION=$(VERSION)
+ ronn -r --manual=khmer --organization='Michigan State University' debian/khmer.1.ronn
+ mkdir l && ln -s /usr/lib/khmer/bin/ ./l/scripts
+
+override_dh_link:
+ dh_link -Xscripts
+
+override_dh_installchangelogs:
+ dh_installchangelogs ChangeLog
Property changes on: trunk/packages/khmer/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/khmer/trunk/debian/source/format
===================================================================
--- trunk/packages/khmer/trunk/debian/source/format (rev 0)
+++ trunk/packages/khmer/trunk/debian/source/format 2015-01-30 17:35:22 UTC (rev 18638)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/khmer/trunk/debian/upstream/metadata
===================================================================
--- trunk/packages/khmer/trunk/debian/upstream/metadata (rev 0)
+++ trunk/packages/khmer/trunk/debian/upstream/metadata 2015-01-30 17:35:22 UTC (rev 18638)
@@ -0,0 +1,12 @@
+Reference:
+ Author: Crusoe et al.
+ Title: The khmer software package: enabling efficient sequence analysis.
+ Journal:
+ Year: 2014
+ Volume:
+ Number:
+ Pages:8
+ DOI: 10.6084/m9.figshare.979190
+ PMID:
+ URL: http://figshare.com/articles/The_khmer_software_package_enabling_efficient_sequence_analysis/979190
+ eprint:
Added: trunk/packages/khmer/trunk/debian/watch
===================================================================
--- trunk/packages/khmer/trunk/debian/watch (rev 0)
+++ trunk/packages/khmer/trunk/debian/watch 2015-01-30 17:35:22 UTC (rev 18638)
@@ -0,0 +1,4 @@
+version=3
+
+opts="downloadurlmangle=s/\/tree\/(.*)/\/archive\/$1.tar.gz/" \
+ https://github.com/ged-lab/khmer/ .*/tree/v([0-9.rc-]+)
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