[med-svn] r6913 - in trunk/packages/dotur/trunk/debian: . manpages.d patches
Thorsten Alteholz
alteholz-guest at alioth.debian.org
Sat Jun 4 18:07:53 UTC 2011
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 <moeller at debian.org> Wed, 02 Mar 2011 23:48:37 +0100
+ -- Thorsten Alteholz <debian at alteholz.de> 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 <moeller at debian.org>
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Steffen Moeller <moeller at debian.org>,
+ Thorsten Alteholz <debian at alteholz.de>
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 <debian at alteholz.de>
+.\"
+.\" 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 <debian at alteholz.de>,
+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 <moeller at debian.org>
+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 <debian at alteholz.de>
+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 <moeller at debian.org>
+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
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