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 <[email protected]> Fri, 02 Jul 2010 12:27:50 +0200 + http://www.mothur.org/wiki/Mothur_manual + + -- Andreas Tille <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]>, Steffen Moeller <[email protected]>, Andreas Tille <[email protected]> -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 <[email protected]> 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 <[email protected]> +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 <[email protected]> + © 2011 Andreas Tille <[email protected]> +License: PD + The packaging work is in the public domain unless stated otherwise. - Patrick Schloss <[email protected]> - Sarah Westcott - -Copyright: - - Copyright (C) 2009 Schloss Lab UMASS Amhers., Patrick Schloss <[email protected]> - -License: - - <Put the license of the package here indented by 4 spaces> - -The Debian packaging is: - - Copyright (C) 2010 Sri Girish Srinivasa Murthy <[email protected]> - -# 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 <[email protected]> # 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
