[med-svn] r5810 - trunk/packages/mothur/trunk/debian
Andreas Tille
tille at alioth.debian.org
Sun Jan 30 11:38:52 UTC 2011
Author: tille
Date: 2011-01-30 11:38:47 +0000 (Sun, 30 Jan 2011)
New Revision: 5810
Added:
trunk/packages/mothur/trunk/debian/README.Source
trunk/packages/mothur/trunk/debian/install
trunk/packages/mothur/trunk/debian/manpages
trunk/packages/mothur/trunk/debian/mothur.1
Removed:
trunk/packages/mothur/trunk/debian/mothur.dirs
trunk/packages/mothur/trunk/debian/mothur.install
Modified:
trunk/packages/mothur/trunk/debian/README.Debian
trunk/packages/mothur/trunk/debian/changelog
trunk/packages/mothur/trunk/debian/control
trunk/packages/mothur/trunk/debian/copyright
trunk/packages/mothur/trunk/debian/menu
trunk/packages/mothur/trunk/debian/rules
trunk/packages/mothur/trunk/debian/watch
Log:
Several polishing, remarks about obtaining source in watch file, NO LICENSE!, manpage
Modified: trunk/packages/mothur/trunk/debian/README.Debian
===================================================================
--- trunk/packages/mothur/trunk/debian/README.Debian 2011-01-30 11:27:42 UTC (rev 5809)
+++ trunk/packages/mothur/trunk/debian/README.Debian 2011-01-30 11:38:47 UTC (rev 5810)
@@ -1,8 +1,10 @@
mothur for Debian
-----------------
-We need help with the man page and other bits, still.
+If you start mothur you can get help by issuing help().
-We found no information whatsoever on the license, yet.
+You also might like to read the online manual at
- -- Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de> Fri, 02 Jul 2010 12:27:50 +0200
+ http://www.mothur.org/wiki/Mothur_manual
+
+ -- Andreas Tille <tille at debian.org> Sun, 30 Jan 2011 00:21:42 +0100
Added: trunk/packages/mothur/trunk/debian/README.Source
===================================================================
--- trunk/packages/mothur/trunk/debian/README.Source (rev 0)
+++ trunk/packages/mothur/trunk/debian/README.Source 2011-01-30 11:38:47 UTC (rev 5810)
@@ -0,0 +1,19 @@
+Hints for mothur on cluster machines:
+-------------------------------------
+
+If you would like to build a mpi-enabled version of mothur, you will
+want to change the no to yes below. If you are running mothur on a
+single machine and not a cluster, the mpi-enabled version is slower than
+using the non-mpi enabled version.
+
+USEMPI ?= no
+
+ifeq ($(strip $(USEMPI)),yes)
+ CXX = mpic++
+ CXXFLAGS += -DUSE_MPI
+endif
+
+(see http://www.mothur.org/wiki/Makefile_options#MPI_Version)
+
+
+ -- Andreas Tille <tille at debian.org> Sun, 30 Jan 2011 00:21:42 +0100
Modified: trunk/packages/mothur/trunk/debian/changelog
===================================================================
--- trunk/packages/mothur/trunk/debian/changelog 2011-01-30 11:27:42 UTC (rev 5809)
+++ trunk/packages/mothur/trunk/debian/changelog 2011-01-30 11:38:47 UTC (rev 5810)
@@ -1,5 +1,7 @@
mothur (1.14.0-1) UNRELEASED; urgency=low
+ UNRELEASED BECAUSE OF MISSING LICENSE STATEMENT
+
* Initial release (Closes: #589675)
-- Andreas Tille <tille at debian.org> Sun, 30 Jan 2011 00:21:42 +0100
Modified: trunk/packages/mothur/trunk/debian/control
===================================================================
--- trunk/packages/mothur/trunk/debian/control 2011-01-30 11:27:42 UTC (rev 5809)
+++ trunk/packages/mothur/trunk/debian/control 2011-01-30 11:38:47 UTC (rev 5810)
@@ -5,7 +5,7 @@
Uploaders: Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>,
Steffen Moeller <moeller at debian.org>,
Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 7), libreadline-dev
+Build-Depends: debhelper (>= 7.1), libreadline-dev, quilt (>= 0.47)
Standards-Version: 3.9.1
Homepage: http://www.mothur.org
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mothur/trunk/?rev=0&sc=0
Modified: trunk/packages/mothur/trunk/debian/copyright
===================================================================
--- trunk/packages/mothur/trunk/debian/copyright 2011-01-30 11:27:42 UTC (rev 5809)
+++ trunk/packages/mothur/trunk/debian/copyright 2011-01-30 11:38:47 UTC (rev 5810)
@@ -1,34 +1,18 @@
-This work was packaged for Debian by:
+Format: http://dep.debian.net/deps/dep5/
+Upstream-Name: Mothur
+Upstream-Contact: http://dep.debian.net/deps/dep5/
+Source: http://www.mothur.org/wiki/Download_mothur
- Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de> on Fri, 02 Jul 2010 12:27:50 +0200
-It was downloaded from http://www.mothur.org
+Files: *
+Copyright: © 2011 Schloss Lab UMASS Amhers., Patrick Schloss <pschloss at umich.edu>
+License: MISSING
+ No license statement was found (neither in code nor web page
+ Upstream was contacted at 2011-01-31
-Upstream Author:
+Files: debian/*
+Copyright: © 2010 Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>
+ © 2011 Andreas Tille <tille at debian.org>
+License: PD
+ The packaging work is in the public domain unless stated otherwise.
- Patrick Schloss <pschloss at umich.edu>
- Sarah Westcott
-
-Copyright:
-
- Copyright (C) 2009 Schloss Lab UMASS Amhers., Patrick Schloss <pschloss at umich.edu>
-
-License:
-
- <Put the license of the package here indented by 4 spaces>
-
-The Debian packaging is:
-
- Copyright (C) 2010 Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>
-
-# Please chose a license for your packaging work. If the program you package
-# uses a mainstream license, using the same license is the safest choice.
-# Please avoid to pick license terms that are more restrictive than the
-# packaged work, as it may make Debian's contributions unacceptable upstream.
-# If you just want it to be GPL version 3, leave the following lines in.
-
-and is licensed under the GPL version 3,
-see `/usr/share/common-licenses/GPL-3'.
-
-# Please also look if there are files or directories which have a
-# different copyright/license attached and list them here.
Copied: trunk/packages/mothur/trunk/debian/install (from rev 5809, trunk/packages/mothur/trunk/debian/mothur.install)
===================================================================
--- trunk/packages/mothur/trunk/debian/install (rev 0)
+++ trunk/packages/mothur/trunk/debian/install 2011-01-30 11:38:47 UTC (rev 5810)
@@ -0,0 +1 @@
+mothur /usr/bin
Added: trunk/packages/mothur/trunk/debian/manpages
===================================================================
--- trunk/packages/mothur/trunk/debian/manpages (rev 0)
+++ trunk/packages/mothur/trunk/debian/manpages 2011-01-30 11:38:47 UTC (rev 5810)
@@ -0,0 +1 @@
+debian/mothur.1
Modified: trunk/packages/mothur/trunk/debian/menu
===================================================================
--- trunk/packages/mothur/trunk/debian/menu 2011-01-30 11:27:42 UTC (rev 5809)
+++ trunk/packages/mothur/trunk/debian/menu 2011-01-30 11:38:47 UTC (rev 5810)
@@ -1,2 +1,3 @@
-?package(mothur):needs="text" section="Applications/Science"\
- title="Mothur" command="/usr/bin/mothur"
+?package(mothur):needs="text" section="Applications/Science/Biology"\
+ title="Mothur" command="/usr/bin/mothur" \
+ hints="sequence analysis suite for research on microbiota"
Added: trunk/packages/mothur/trunk/debian/mothur.1
===================================================================
--- trunk/packages/mothur/trunk/debian/mothur.1 (rev 0)
+++ trunk/packages/mothur/trunk/debian/mothur.1 2011-01-30 11:38:47 UTC (rev 5810)
@@ -0,0 +1,25 @@
+.TH MOTHUR 1 "2011-01-30"
+.SH NAME
+mothur \- sequence analysis suite for research on microbiota
+.SH SYNOPSIS
+.B mothur
+[ batchfile ]
+.SH DESCRIPTION
+This manual page documents briefly the
+.B mothur
+command.
+.PP
+\fBMothur\fP seeks to develop a single piece of open-source, expandable
+software to fill the bioinformatics needs of the microbial ecology
+community. It has incorporated the functionality of dotur, sons,
+treeclimber, s-libshuff, unifrac, and much more. In addition to improving
+the flexibility of these algorithms, a number of other features including
+calculators and visualization tools were added.
+.SH SEE ALSO
+Online manual
+.BR http://www.mothur.org/wiki/Mothur_manual
+.SH AUTHOR
+#PACKAGE# was written by <upstream author>.
+.PP
+This manual page was written by #USERNAME# <#EMAIL#>,
+for the Debian project (and may be used by others).
Deleted: trunk/packages/mothur/trunk/debian/mothur.dirs
===================================================================
--- trunk/packages/mothur/trunk/debian/mothur.dirs 2011-01-30 11:27:42 UTC (rev 5809)
+++ trunk/packages/mothur/trunk/debian/mothur.dirs 2011-01-30 11:38:47 UTC (rev 5810)
@@ -1 +0,0 @@
-/usr/bin
Deleted: trunk/packages/mothur/trunk/debian/mothur.install
===================================================================
--- trunk/packages/mothur/trunk/debian/mothur.install 2011-01-30 11:27:42 UTC (rev 5809)
+++ trunk/packages/mothur/trunk/debian/mothur.install 2011-01-30 11:38:47 UTC (rev 5810)
@@ -1 +0,0 @@
-./mothur /usr/bin
Modified: trunk/packages/mothur/trunk/debian/rules
===================================================================
--- trunk/packages/mothur/trunk/debian/rules 2011-01-30 11:27:42 UTC (rev 5809)
+++ trunk/packages/mothur/trunk/debian/rules 2011-01-30 11:38:47 UTC (rev 5810)
@@ -1,53 +1,24 @@
#!/usr/bin/make -f
-# -*- makefile -*-
-# Sample debian/rules that uses debhelper.
-# This file was originally written by Joey Hess and Craig Small.
-# As a special exception, when this file is copied by dh-make into a
-# dh-make output file, you may use that output file without restriction.
-# This special exception was added by Craig Small in version 0.37 of dh-make.
+# Sample debian/rules for mothur
+# Andreas Tille <tille at debian.org>
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
-build: build-stamp
+ARCHBITS ?= $(shell dpkg-architecture -qDEB_BUILD_ARCH_BITS)
-build-stamp:
- make 64BIT_VERSION=yes
- touch $@
+%:
+ dh $@ --with quilt
-install: build-stamp
+override_dh_auto_build:
+ if [ $(ARCHBITS) -eq 64 ] ; then \
+ $(MAKE) 64BIT_VERSION=yes ; \
+ else \
+ $(MAKE) ; \
+ fi
-binary: build install
- dh_testdir
- dh_testroot
- dh_installchangelogs
- dh_installdocs
- dh_installexamples
+override_dh_auto_install:
dh_install
- dh_installmenu
-# dh_desktop
-# dh_python
- dh_installman
- dh_link
- dh_strip
- dh_compress
- dh_fixperms
- dh_makeshlibs
- dh_installdeb
- dh_shlibdeps
- dh_gencontrol
- dh_md5sums
- dh_builddeb
-clean:
- dh_clean
-
-
-#UPSTREAM_VERSION=1.12.3
-UPSTREAM_VERSION=$(shell dpkg-parsechangelog | grep ^Version: | cut -f 2 -d \ | cut -f 1 -d -)
-
-test:
- echo 'UPSTREAM_VESRION="$(UPSTREAM_VERSION)"'
-
get-orig-source:
. debian/get-orig-source
Modified: trunk/packages/mothur/trunk/debian/watch
===================================================================
--- trunk/packages/mothur/trunk/debian/watch 2011-01-30 11:27:42 UTC (rev 5809)
+++ trunk/packages/mothur/trunk/debian/watch 2011-01-30 11:38:47 UTC (rev 5810)
@@ -1,3 +1,6 @@
+## Warning: Mothur only numbere *previous* releases.
+## The current release downloadable archive does not feature a version number
+
version=3
http://www.mothur.org/wiki/Download_mothur \
/w/images/.*/.*/Mothur\.([\d\.]+)\.zip
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