[med-svn] r6846 - in trunk/packages/prank/trunk: . debian debian/patches debian/source
Manuel Prinz
manuel at alioth.debian.org
Fri May 20 09:17:19 UTC 2011
Author: manuel
Date: 2011-05-20 09:17:15 +0000 (Fri, 20 May 2011)
New Revision: 6846
Added:
trunk/packages/prank/trunk/debian/
trunk/packages/prank/trunk/debian/changelog
trunk/packages/prank/trunk/debian/compat
trunk/packages/prank/trunk/debian/control
trunk/packages/prank/trunk/debian/copyright
trunk/packages/prank/trunk/debian/patches/
trunk/packages/prank/trunk/debian/patches/fix-broken-clean-target.patch
trunk/packages/prank/trunk/debian/patches/manpage-for-prank.patch
trunk/packages/prank/trunk/debian/patches/series
trunk/packages/prank/trunk/debian/prank.install
trunk/packages/prank/trunk/debian/prank.manpages
trunk/packages/prank/trunk/debian/rules
trunk/packages/prank/trunk/debian/source/
trunk/packages/prank/trunk/debian/source/format
trunk/packages/prank/trunk/debian/watch
Log:
[svn-inject] Applying Debian modifications (100802-1) to trunk
Property changes on: trunk/packages/prank/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/prank/trunk/debian/changelog
===================================================================
--- trunk/packages/prank/trunk/debian/changelog (rev 0)
+++ trunk/packages/prank/trunk/debian/changelog 2011-05-20 09:17:15 UTC (rev 6846)
@@ -0,0 +1,5 @@
+prank (100802-1) UNRELEASED; urgency=low
+
+ * Initial release. (Closes: #XXXXXX)
+
+ -- Manuel Prinz <manuel at debian.org> Fri, 20 May 2011 10:52:25 +0200
Added: trunk/packages/prank/trunk/debian/compat
===================================================================
--- trunk/packages/prank/trunk/debian/compat (rev 0)
+++ trunk/packages/prank/trunk/debian/compat 2011-05-20 09:17:15 UTC (rev 6846)
@@ -0,0 +1 @@
+8
Added: trunk/packages/prank/trunk/debian/control
===================================================================
--- trunk/packages/prank/trunk/debian/control (rev 0)
+++ trunk/packages/prank/trunk/debian/control 2011-05-20 09:17:15 UTC (rev 6846)
@@ -0,0 +1,24 @@
+Source: prank
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Manuel Prinz <manuel at debian.org>
+Build-Depends: debhelper (>= 8)
+Standards-Version: 3.9.2
+Homepage: http://www.ebi.ac.uk/goldman-srv/prank/
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/prank/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/prank/trunk/?rev=0&sc=0
+
+Package: prank
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Probabilistic Alignment Kit for biological sequences
+ PRANK is a probabilistic multiple alignment program for DNA, codon and
+ amino-acid sequences. It's based on a novel algorithm that treats insertions
+ correctly and avoids over-estimation of the number of deletion events.
+ .
+ In addition, PRANK borrows ideas from maximum likelihood methods used in
+ phylogenetics and correctly takes into account the evolutionary distances
+ between sequences. Lastly, PRANK allows for defining a potential structure
+ for sequences to be aligned and then, simultaneously with the alignment,
+ predicts the locations of structural units in the sequences.
Added: trunk/packages/prank/trunk/debian/copyright
===================================================================
--- trunk/packages/prank/trunk/debian/copyright (rev 0)
+++ trunk/packages/prank/trunk/debian/copyright 2011-05-20 09:17:15 UTC (rev 6846)
@@ -0,0 +1,42 @@
+This work was packaged for Debian by:
+
+ Manuel Prinz <manuel at debian.org> on Wed, 16 Feb 2011 14:49:47 +0100
+
+It was downloaded from:
+
+ http://www.ebi.ac.uk/goldman-srv/prank/src/prank/
+
+Upstream Author:
+
+ Ari Loytynoja
+
+Copyright:
+
+ Copyright © 2005 Ari Loytynoja
+
+License:
+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+
+On Debian systems, the complete text of the GNU General
+Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+The Debian packaging is:
+
+ Copyright © 2011 Manuel Prinz <manuel at debian.org>
+
+you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
Added: trunk/packages/prank/trunk/debian/patches/fix-broken-clean-target.patch
===================================================================
--- trunk/packages/prank/trunk/debian/patches/fix-broken-clean-target.patch (rev 0)
+++ trunk/packages/prank/trunk/debian/patches/fix-broken-clean-target.patch 2011-05-20 09:17:15 UTC (rev 6846)
@@ -0,0 +1,14 @@
+--- a/Makefile
++++ b/Makefile
+@@ -107,9 +107,10 @@
+ $(TARGET): $(OBJECTS)
+ $(LINK) -o $(TARGET) $(OBJECTS) $(LIBS)
+
+-clean:clean
++clean:
+ -$(DEL_FILE) $(OBJECTS)
+ -$(DEL_FILE) *~ core *.core
++ -$(DEL_FILE) $(TARGET)
+
+ ####### Compile
+
Added: trunk/packages/prank/trunk/debian/patches/manpage-for-prank.patch
===================================================================
--- trunk/packages/prank/trunk/debian/patches/manpage-for-prank.patch (rev 0)
+++ trunk/packages/prank/trunk/debian/patches/manpage-for-prank.patch 2011-05-20 09:17:15 UTC (rev 6846)
@@ -0,0 +1,204 @@
+--- a/Makefile
++++ b/Makefile
+@@ -8,6 +8,7 @@
+ LINK = g++
+ LIBS = -L/usr/lib
+ DEL_FILE = rm -f
++POD2MAN = pod2man --utf8 --center "The Probabilistic Alignment Kit" -release="v.100802"
+
+ ####### Output directory
+
+@@ -80,6 +81,8 @@
+
+ TARGET = prank
+
++MANPAGES = prank.1
++
+ first: all
+ ####### Implicit rules
+
+@@ -102,7 +105,7 @@
+
+ ####### Build rules
+
+-all: Makefile $(TARGET)
++all: Makefile $(TARGET) $(MANPAGES)
+
+ $(TARGET): $(OBJECTS)
+ $(LINK) -o $(TARGET) $(OBJECTS) $(LIBS)
+@@ -111,6 +114,7 @@
+ -$(DEL_FILE) $(OBJECTS)
+ -$(DEL_FILE) *~ core *.core
+ -$(DEL_FILE) $(TARGET)
++ -$(DEL_FILE) $(MANPAGES)
+
+ ####### Compile
+
+@@ -479,3 +483,10 @@
+
+ writefile.o: writefile.cpp writefile.h
+ $(CXX) -c $(CXXFLAGS) $(INCPATH) -o writefile.o writefile.cpp
++
++####### Manpages
++
++%.1: %.1.pod
++ $(POD2MAN) --section=1 --name="$(shell basename $@ .1 | tr a-z A-Z)" $< >$@
++
++doc: $(MANPAGES)
+--- /dev/null
++++ b/prank.1.pod
+@@ -0,0 +1,154 @@
++=head1 NAME
++
++prank - Computes probabilistic multiple sequence alignments
++
++=head1 SYNOPSIS
++
++B<prank> I<sequence_file>
++
++B<prank> [optional parameters] -d=I<sequence_file> [optional parameters]
++
++=head1 DESCRIPTION
++
++The Probabilistic Alignment Kit (PRANK) is a probabilistic multiple alignment
++program for DNA, codon and amino-acid sequences. It's based on a novel algorithm
++that treats insertions correctly and avoids over-estimation of the number of
++deletion events.
++
++In addition, PRANK borrows ideas from maximum likelihood methods used in
++phylogenetics and correctly takes into account the evolutionary distances
++between sequences. Lastly, PRANK allows for defining a potential structure for
++sequences to be aligned and then, simultaneously with the alignment, predicts
++the locations of structural units in the sequences.
++
++=head1 OPTIONS
++
++=head2 INPUT/OUTPUT PARAMETERS
++
++=over 8
++
++=item B<-d=I<sequence_file>>
++
++The input sequence file in FASTA format.
++
++=item B<-t=I<tree_file>>
++
++The tree file to use. If unset, an appriximated NJ tree is generated.
++
++=item B<-m=I<model_file>>
++
++The model file to use. If unset, I<model_file> is set to B<HKY2/WAG>.
++
++=item B<-o=I<output_file>>
++
++Set the name of the output file. If unset, I<output_file> is set to B<output>.
++
++=item B<-f=I<output_format>>
++
++Set the output format. I<output_format> can be one of B<fasta> (default),
++B<phylipi>, B<phylips>, B<paml>, or B<nexus>.
++
++=item B<-shortnames>
++
++Truncate names at first space character.
++
++=item B<-quiet>
++
++Reduce output.
++
++=back
++
++=head2 MODEL PARAMETERS
++
++=over 8
++
++=item B<-F>, B<+F>
++
++Force insertions to be always skipped.
++
++=item B<-gaprate=I<#>>
++
++Set the gap opening rate. The default is B<0.025> for DNA and B<0.005> for
++proteins.
++
++=item B<-gapext=I<#>>
++
++Set the gap extension probability. The default is B<0.75> for DNA and B<0.5> for
++proteins.
++
++=item B<-codon>
++
++Use empirical codon model for coding DNA.
++
++=item B<-DNA>, B<-protein>
++
++Use DNA or protein model, respectively. Disables auto-detection of model.
++
++=item B<-termgap>
++
++Penalise terminal gaps normally.
++
++=item B<-nomissing>
++
++No missing data. Use B<-F> for terminal gaps.
++
++=item B<-e>
++
++Do not remove gaps from pre-aligned sequences.
++
++=back
++
++=head2 OTHER PARAMETERS
++
++=over 8
++
++=item B<-nopost>
++
++Do not compute posterior support. The default is to compute it.
++
++=item B<-once>
++
++Run only once. The default is to run twice if no guidetree is given.
++
++=item B<-twice>
++
++Run twice always.
++
++=item B<-prunetree>
++
++Prune guide tree branches with no sequence data.
++
++=item B<-uselogs>
++
++Slower but should work for a greater number of sequences.
++
++=item B<-translate>
++
++Translate input data to protein sequences.
++
++=item B<-mttranslate>
++
++Translate input data to protein sequencess using mt table.
++
++=item B<-maxpairdist=I<#>>
++
++Maximum pairwise distance for matrix computation.
++
++=item B<-convert>
++
++Do not align, just convert to a different format.
++
++=item B<-help>
++
++Show an extended help page with more options.
++
++=back
++
++=head1 AUTHORS
++
++B<prank> was written by Ari Loytynoja.
++
++This manual page was written by Manuel Prinz <manuel at debian.org> for the Debian
++project (and may be used by others).
++
++=cut
Added: trunk/packages/prank/trunk/debian/patches/series
===================================================================
--- trunk/packages/prank/trunk/debian/patches/series (rev 0)
+++ trunk/packages/prank/trunk/debian/patches/series 2011-05-20 09:17:15 UTC (rev 6846)
@@ -0,0 +1,2 @@
+fix-broken-clean-target.patch
+manpage-for-prank.patch
Added: trunk/packages/prank/trunk/debian/prank.install
===================================================================
--- trunk/packages/prank/trunk/debian/prank.install (rev 0)
+++ trunk/packages/prank/trunk/debian/prank.install 2011-05-20 09:17:15 UTC (rev 6846)
@@ -0,0 +1 @@
+prank usr/bin/
Added: trunk/packages/prank/trunk/debian/prank.manpages
===================================================================
--- trunk/packages/prank/trunk/debian/prank.manpages (rev 0)
+++ trunk/packages/prank/trunk/debian/prank.manpages 2011-05-20 09:17:15 UTC (rev 6846)
@@ -0,0 +1 @@
+prank.1
Added: trunk/packages/prank/trunk/debian/rules
===================================================================
--- trunk/packages/prank/trunk/debian/rules (rev 0)
+++ trunk/packages/prank/trunk/debian/rules 2011-05-20 09:17:15 UTC (rev 6846)
@@ -0,0 +1,4 @@
+#!/usr/bin/make -f
+
+%:
+ dh $@
Property changes on: trunk/packages/prank/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/prank/trunk/debian/source/format
===================================================================
--- trunk/packages/prank/trunk/debian/source/format (rev 0)
+++ trunk/packages/prank/trunk/debian/source/format 2011-05-20 09:17:15 UTC (rev 6846)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/prank/trunk/debian/watch
===================================================================
--- trunk/packages/prank/trunk/debian/watch (rev 0)
+++ trunk/packages/prank/trunk/debian/watch 2011-05-20 09:17:15 UTC (rev 6846)
@@ -0,0 +1,2 @@
+version=3
+http://www.ebi.ac.uk/goldman-srv/prank/src/prank/prank\.src\.(\d{6})\.tgz
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