[med-svn] r6183 - trunk/packages/seq-gen/trunk/debian

Mon Mar 7 16:03:26 UTC 2011

Author: malex-guest
Date: 2011-03-07 16:03:21 +0000 (Mon, 07 Mar 2011)
New Revision: 6183

Added:
   trunk/packages/seq-gen/trunk/debian/seq-gen.1
Modified:
   trunk/packages/seq-gen/trunk/debian/control
   trunk/packages/seq-gen/trunk/debian/copyright
   trunk/packages/seq-gen/trunk/debian/rules
   trunk/packages/seq-gen/trunk/debian/seq-gen-doc.install
Log:
manual page , copyright & minor changes.



Modified: trunk/packages/seq-gen/trunk/debian/control
===================================================================

--- trunk/packages/seq-gen/trunk/debian/control	2011-03-07 16:01:48 UTC (rev 6182)
+++ trunk/packages/seq-gen/trunk/debian/control	2011-03-07 16:03:21 UTC (rev 6183)
@@ -27,4 +27,9 @@
 Package: seq-gen-doc
 Architecture: all
 Description: documentation for seq-gen
+ Seq-Gen is a program that will simulate the evolution of nucleotide
+ or amino acid sequences along a phylogeny, using common models of the
+ substitution process.
+ .
+ This package contains the documentation for seq-gen
  

Modified: trunk/packages/seq-gen/trunk/debian/copyright
===================================================================
--- trunk/packages/seq-gen/trunk/debian/copyright	2011-03-07 16:01:48 UTC (rev 6182)
+++ trunk/packages/seq-gen/trunk/debian/copyright	2011-03-07 16:03:21 UTC (rev 6183)
@@ -3,10 +3,42 @@
 Source: <url://example.com>
 
 Files: *
-Copyright: <years> <put author's name and email here>
-           <years> <likewise for another author>
-License: GPL-3.0+
+Copyright: Copyright (c)1996-2004, Andrew Rambaut & Nick Grassly
+   Department of Zoology, University of Oxford                  
+   All rights reserved.                          
 
+License: 
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+   1. Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+
+   2. 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.
+
+   3. The names of its contributors may not 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 OWNER 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.
+
+ Any feedback is very welcome.
+ http://evolve.zoo.ox.ac.uk/software/Seq-Gen/
+ email: andrew.rambaut at zoo.ox.ac.uk
+
 Files: debian/*
 Copyright: 2011 Alex Mestiashvili <alex at biotec.tu-dresden.de>
 License: GPL-3.0+
@@ -27,14 +59,3 @@
  .
  On Debian systems, the complete text of the GNU General
  Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
-
-# Please choose 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 line in.
-
-and is licensed under the GPL version 3, see above.
-
-# Please also look if there are files or directories which have a
-# different copyright/license attached and list them here.

Modified: trunk/packages/seq-gen/trunk/debian/rules
===================================================================
--- trunk/packages/seq-gen/trunk/debian/rules	2011-03-07 16:01:48 UTC (rev 6182)
+++ trunk/packages/seq-gen/trunk/debian/rules	2011-03-07 16:03:21 UTC (rev 6183)
@@ -10,3 +10,6 @@
 
 %:
 	dh $@ --sourcedirectory=source
+
+override_dh_installchangelogs:
+    dh_installchangelogs documentation/Using_Seq-Gen_with_PAUP

Modified: trunk/packages/seq-gen/trunk/debian/seq-gen-doc.install
===================================================================
--- trunk/packages/seq-gen/trunk/debian/seq-gen-doc.install	2011-03-07 16:01:48 UTC (rev 6182)
+++ trunk/packages/seq-gen/trunk/debian/seq-gen-doc.install	2011-03-07 16:03:21 UTC (rev 6183)
@@ -1 +1,3 @@
-#DOCS#
+documentation/Seq-Gen.Manual.html 	usr/share/doc/seq-gen/
+documentation/Using_Seq-Gen_with_PAUP	usr/share/doc/seq-gen/
+

Added: trunk/packages/seq-gen/trunk/debian/seq-gen.1
===================================================================
--- trunk/packages/seq-gen/trunk/debian/seq-gen.1	                        (rev 0)
+++ trunk/packages/seq-gen/trunk/debian/seq-gen.1	2011-03-07 16:03:21 UTC (rev 6183)
@@ -0,0 +1,81 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.38.2.
+.TH SEQ-GEN "1" "March 2011" "seq-gen 1.3.2" "User Commands"
+.SH NAME
+seq-gen \- Sequence Generator
+.SH SYNOPSIS
+.B seq-gen
+[\fI-m MODEL\fR] [\fI-l #\fR] [\fI-n #\fR] [\fI-p #\fR] [\fI-s # | -d #\fR] [\fI-k #\fR][\-c #1 #2 #3 | \-a\fR # [\-g #]] [\-f e | #] [\-t # | \-r\fR #][\-z #] [\-o[p][r][n]] [\-w[a][r]] [\-x NAME] [\-q] [\-h] [treefile]
+.SH DESCRIPTION
+Sequence Generator \- seq\-gen
+Version 1.3.2
+.IP
+.HP
+\fB\-l\fR: # = sequence length [default = 1000].
+.HP
+\fB\-n\fR: # = simulated datasets per tree [default = 1].
+.HP
+\fB\-p\fR: # = number of partitions (and trees) per sequence [default = 1].
+.HP
+\fB\-s\fR: # = branch length scaling factor [default = 1.0].
+.HP
+\fB\-d\fR: # = total tree scale [default = use branch lengths].
+.HP
+\fB\-k\fR: # = use sequence k as ancestral (needs alignment) [default = random].
+.IP
+Substitution model options:
+.HP
+\fB\-m\fR: MODEL = HKY, F84, GTR, JTT, WAG, PAM, BLOSUM, MTREV, GENERAL
+.IP
+HKY, F84 & GTR are for nucleotides the rest are for amino acids
+.HP
+\fB\-a\fR: # = shape (alpha) for gamma rate heterogeneity [default = none].
+.HP
+\fB\-g\fR: # = number of gamma rate categories [default = continuous].
+.HP
+\fB\-i\fR: # = proportion of invariable sites [default = 0.0].
+.IP
+Nucleotid model specific options:
+.HP
+\fB\-c\fR: #1 #2 #3 = rates for codon position heterogeneity [default = none].
+.HP
+\fB\-t\fR: # = transition\-transversion ratio [default = equal rate].
+.HP
+\fB\-r\fR: #1 #2 #3 #4 #5 #6= general rate matrix [default = all 1.0].
+.HP
+\fB\-f\fR: #A #C #G #T = nucleotide frequencies [default = all equal].
+.IP
+Amino Acid model specific options:
+.IP
+specify using the order ARNDCQEGHILKMFPSTWYV
+.HP
+\fB\-r\fR: #1 .. #190 = general rate matrix [default = all 1.0].
+.HP
+\fB\-f\fR: #1 .. #20 = amino acid frequencies e=equal [default = matrix freqs].
+.IP
+Miscellaneous options:
+.HP
+\fB\-z\fR: # = seed for random number generator [default = system generated].
+.HP
+\fB\-o\fR: Output file format [default = PHYLIP]
+.IP
+p PHYLIP format
+r relaxed PHYLIP format
+n NEXUS format
+.HP
+\fB\-w\fR: Write additional information [default = none]
+.IP
+a Write ancestral sequences for each node
+r Write rate for each site
+.HP
+\fB\-x\fR: NAME = a text file to insert after every dataset [default = none].
+.HP
+\fB\-h\fR: Give this help message
+.HP
+\fB\-q\fR: Quiet
+.IP
+treefile: name of tree file [default = trees on stdin]
+.SH AUTHOR
+(c) Copyright, 1996\-2004 Andrew Rambaut and Nick Grassly
+Department of Zoology, University of Oxford
+South Parks Road, Oxford OX1 3PS, U.K.
+


