Author: alteholz-guest Date: 2011-06-04 18:07:53 +0000 (Sat, 04 Jun 2011) New Revision: 6913
Added: trunk/packages/dotur/trunk/debian/manpages trunk/packages/dotur/trunk/debian/manpages.d/ trunk/packages/dotur/trunk/debian/manpages.d/dotur.1 trunk/packages/dotur/trunk/debian/patches/changelog.patch Modified: trunk/packages/dotur/trunk/debian/changelog trunk/packages/dotur/trunk/debian/control trunk/packages/dotur/trunk/debian/copyright trunk/packages/dotur/trunk/debian/patches/Makefile.patch trunk/packages/dotur/trunk/debian/patches/compilation.patch trunk/packages/dotur/trunk/debian/patches/series Log: cleaning up dotur Modified: trunk/packages/dotur/trunk/debian/changelog =================================================================== --- trunk/packages/dotur/trunk/debian/changelog 2011-06-04 18:02:04 UTC (rev 6912) +++ trunk/packages/dotur/trunk/debian/changelog 2011-06-04 18:07:53 UTC (rev 6913) @@ -1,5 +1,5 @@ -dotur (1.53-1) UNRELEAED; urgency=low +dotur (1.53-1) unstable; urgency=low - * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP> + * Initial release (Closes: #12345) - -- Steffen Moeller <[email protected]> Wed, 02 Mar 2011 23:48:37 +0100 + -- Thorsten Alteholz <[email protected]> Fri, 03 Jun 2011 16:00:00 +0200 Modified: trunk/packages/dotur/trunk/debian/control =================================================================== --- trunk/packages/dotur/trunk/debian/control 2011-06-04 18:02:04 UTC (rev 6912) +++ trunk/packages/dotur/trunk/debian/control 2011-06-04 18:07:53 UTC (rev 6913) @@ -1,9 +1,12 @@ Source: dotur Section: science Priority: extra -Maintainer: Steffen Moeller <[email protected]> +Maintainer: Debian Med Packaging Team <[email protected]> +DM-Upload-Allowed: yes +Uploaders: Steffen Moeller <[email protected]>, + Thorsten Alteholz <[email protected]> Build-Depends: debhelper (>= 7.0.50~) -Standards-Version: 3.9.1 +Standards-Version: 3.9.2 Homepage: http://www.plantpath.wisc.edu/fac/joh/DOTUR/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/dotur/trunk/?rev=0&sc=0 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/dotur/trunk/ Modified: trunk/packages/dotur/trunk/debian/copyright =================================================================== --- trunk/packages/dotur/trunk/debian/copyright 2011-06-04 18:02:04 UTC (rev 6912) +++ trunk/packages/dotur/trunk/debian/copyright 2011-06-04 18:07:53 UTC (rev 6913) @@ -1,10 +1,9 @@ Format: http://dep.debian.net/deps/dep5 Upstream-Name: dotur -Source: <url://example.com> +Source: http://www.plantpath.wisc.edu/fac/joh/DOTUR/ Files: * -Copyright: <years> <put author's name and email here> - <years> <likewise for another author> +Copyright: 2004-2005 Patrick D. Schlos License: GPL-2.0+ Files: debian/* @@ -27,6 +26,3 @@ . On Debian systems, the complete text of the GNU General Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". - -# Please also look if there are files or directories which have a -# different copyright/license attached and list them here. Added: trunk/packages/dotur/trunk/debian/manpages =================================================================== --- trunk/packages/dotur/trunk/debian/manpages (rev 0) +++ trunk/packages/dotur/trunk/debian/manpages 2011-06-04 18:07:53 UTC (rev 6913) @@ -0,0 +1 @@ +debian/manpages.d/dotur.1 Added: trunk/packages/dotur/trunk/debian/manpages.d/dotur.1 =================================================================== --- trunk/packages/dotur/trunk/debian/manpages.d/dotur.1 (rev 0) +++ trunk/packages/dotur/trunk/debian/manpages.d/dotur.1 2011-06-04 18:07:53 UTC (rev 6913) @@ -0,0 +1,62 @@ +'\" t +.\" ** The above line should force tbl to be a preprocessor ** +.\" Copyright (C), 2011, Thorsten Alteholz <[email protected]> +.\" +.\" You may distribute under the terms of the GNU General Public +.\" License as specified in the file COPYING that comes with the +.\" man_db distribution. +.\" +.\" +.TH Dotur 1 "June 03, 2011" "DOTUR" +.SH NAME +.B dotur +\- A program for calculating discriptive statistics for sequence libraries + +.SH SYNOPSIS +.B dotur +[\fI-i Iterations (<1000>)\fR] [\fI-c ClusterMethod (<f>, n, a)\fR] [\fI-p Precision (10, <100>, 1000, 10000)\fR] [\fI-l\fR] [\fI-j\fR] \fI<file>\fR +.SH OPTIONS +.TP +\fB\-i\fR: +Number of iterations (default = 1000) +.TP +\fB\-c\fR: +Clustering method \- (f) furthest neighbor, (n) nearest neighbor, +(a) average neighbor (default = f) +.TP +\fB\-p\fR: +Precision of distances for output, increasing can dramatically +lengthen execution times \- 10, 100, 1000, 10000 (default = 100) +.TP +\fB\-l\fR: +Input file is lower triangular (default = square matrix) +.TP +\fB\-r\fR: +Calculates rarefaction curves for each parameter, can dramatically +lengthen execution times. Simple rarefaction curve always calculated. +.HP +\fB\-stop\fR: Stops clustering when cutoff has been reached. +.HP +\fB\-wrep\fR: Samples with replacement. +.TP +\fB\-jumble\fR: +Jumble the order of the distance matrix. +.TP +\fB\-sim\fR: +Converts similarity score to distance (D=1\-S). + +.SH DESCRIPTION +This is the Debian GNU/Linux version of dotur. + +DOTUR is a computer program that takes a distance matrix describing +the genetic distance between DNA sequence data and assigns sequences to +operational taxonomic units (OTUs) using either the furthest, average, +or nearest neighbor algorithms for all possible distances that can be +described using the distance matrix. Using the OTU composition data, +DOTUR constructs collector's and rarefaction curves for sampling +intensity, richness estimators, and diversity indices. + +.SH AUTHOR +This manual page was compiled from the package description +and the output of help2man by Thorsten Alteholz <[email protected]>, +for the Debian GNU/Linux system (but may be used by others). Modified: trunk/packages/dotur/trunk/debian/patches/Makefile.patch =================================================================== --- trunk/packages/dotur/trunk/debian/patches/Makefile.patch 2011-06-04 18:02:04 UTC (rev 6912) +++ trunk/packages/dotur/trunk/debian/patches/Makefile.patch 2011-06-04 18:07:53 UTC (rev 6913) @@ -1,3 +1,6 @@ +Description: Create new Makfile for dotur.C +Author: Steffen Moeller <[email protected]> +Last-Update: 2011-03-03 Index: dotur-1.53/Makefile =================================================================== --- /dev/null 1970-01-01 00:00:00.000000000 +0000 Added: trunk/packages/dotur/trunk/debian/patches/changelog.patch =================================================================== --- trunk/packages/dotur/trunk/debian/patches/changelog.patch (rev 0) +++ trunk/packages/dotur/trunk/debian/patches/changelog.patch 2011-06-04 18:07:53 UTC (rev 6913) @@ -0,0 +1,54 @@ +Description: Create upstream changelog (extracted from README) +Author: Thorsten Alteholz <[email protected]> +Last-Update: 2011-06-03 +Index: dotur-1.53/changelog +=================================================================== +--- /dev/null 1970-01-01 00:00:00.000000000 +0000 ++++ dotur-1.53/changelog 2011-06-03 12:55:46.000000000 +0200 +@@ -0,0 +1,45 @@ ++Version 1.0 ++ Released May 25, 2004 ++Version 1.1 ++ Released July 19, 2004 ++ Fixed bug in shannon index files ++ expanded number of values to the right of the decimal point from 2 to 4 ++Version 1.2 ++ Released August 23, 2004 ++ Fixed bug in calculating variance of shannon index ++ Give user the flexibility to set the number of iterations to run ++ Reverted to presenting the mean instead of 50%tile for rarefaction curve ++ Fixed a small bug that had rarefaction curves going through (1,0) instead of (1,1) ++ Changed *.r_rarefaction filename to *.rarefaction ++ Changed *.r_*.ltt to *.ltt filenames (eg. *r_chao.ltt is now *.chao.ltt) ++ Wrote first version of user manual ++Version 1.3 ++ Released March 3, 2005 ++ Final release before publication of paper in March 2005 issue of AEM ++ Fixed libraries dependency error that caused compilation problems on some platforms ++ Fixed core dump error received by some users ++ Fixed bugs in reporting Shannon & Simpson Indices ++ Changed number of places to report right of the decimal point for output files ++ Streamlined terminal output ++ Added user control of whether to calculate rarefaction curve for ecological parameters ++ (still calcuates traditional rarefaction curve) - makes execution much faster ++ Fixed some problems and updated parts of user manual ++Version 1.4 ++ Released March 8, 2005 ++ Fixed bug in calculating the confidence interval for the Chao1 estimator ++Version 1.5 ++ Released April 19, 2005 ++ Added 95% CI for ACE richness estimator ++ Updated bias-corrected Chao1 richness estimator and standard error formulae according to Colwell and Chao ++ Allow user to set largest distance to consider (-stop) ++ Allow user to construct a rarefaction curve obtained by sampling with replacement (-wrep) ++ Fixed a problem in constructing collector's curves caused by sequence names that are a fragment of another name ++Version 1.51 ++ Released April 22, 2005 ++ Support mega3 formatted distance files as input ++Version 1.53 ++ Released November XX, 2005 ++ Allow user to "jumble" the order of sequences in the distance matrix (use -jumble) ++ Allow the user to input a similarity matrix, although correction is still recommended (use -sim) ++ Modified data types in otu.h making the clustering procedure use less memory and faster ++ DOTUR now produces a file containing data to construct rank-abundance plots + Modified: trunk/packages/dotur/trunk/debian/patches/compilation.patch =================================================================== --- trunk/packages/dotur/trunk/debian/patches/compilation.patch 2011-06-04 18:02:04 UTC (rev 6912) +++ trunk/packages/dotur/trunk/debian/patches/compilation.patch 2011-06-04 18:07:53 UTC (rev 6913) @@ -1,3 +1,6 @@ +Description: Add new includes to be able to compile with current g++ +Author: Steffen Moeller <[email protected]> +Last-Update: 2011-03-03 Index: dotur-1.53/dotur.C =================================================================== --- dotur-1.53.orig/dotur.C 2011-03-03 00:04:37.000000000 +0100 Modified: trunk/packages/dotur/trunk/debian/patches/series =================================================================== --- trunk/packages/dotur/trunk/debian/patches/series 2011-06-04 18:02:04 UTC (rev 6912) +++ trunk/packages/dotur/trunk/debian/patches/series 2011-06-04 18:07:53 UTC (rev 6913) @@ -1,2 +1,3 @@ Makefile.patch compilation.patch +changelog.patch _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
