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 <[email protected]> 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 <[email protected]> +Uploaders: Manuel Prinz <[email protected]> +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 <[email protected]> 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 <[email protected]> + +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 <[email protected]> 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
