[med-svn] r12097 - in trunk/packages/prank/trunk/debian: . patches
Timothy Booth
tbooth-guest at alioth.debian.org
Mon Aug 20 14:41:22 UTC 2012
Author: tbooth-guest
Date: 2012-08-20 14:41:22 +0000 (Mon, 20 Aug 2012)
New Revision: 12097
Added:
trunk/packages/prank/trunk/debian/README.source
Removed:
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
Modified:
trunk/packages/prank/trunk/debian/changelog
trunk/packages/prank/trunk/debian/control
trunk/packages/prank/trunk/debian/copyright
trunk/packages/prank/trunk/debian/rules
trunk/packages/prank/trunk/debian/watch
Log:
Sadly this is still not certified free due to the PAML license
ambiguity.
However, I've make the changes necessary to build the latest
source and logged the license issue on Google code.
Added: trunk/packages/prank/trunk/debian/README.source
===================================================================
--- trunk/packages/prank/trunk/debian/README.source (rev 0)
+++ trunk/packages/prank/trunk/debian/README.source 2012-08-20 14:41:22 UTC (rev 12097)
@@ -0,0 +1,10 @@
+The upstream currently ships with both a Makefile and a Makefile.qt.
+
+The default build approach would be to re-make the Makefile from the
+.qt template, but in fact the Makefile has been manually tuned by
+upstream. Therefore I keep the orignal Makefile and prevent DH from
+invoking removing the Makefile on cleanup.
+
+Not sure if this was the "best" fix but it's the easiest.
+
+-- Tim Booth <tbooth at ceh.ac.uk> Aug 2012
Modified: trunk/packages/prank/trunk/debian/changelog
===================================================================
--- trunk/packages/prank/trunk/debian/changelog 2012-08-20 13:40:51 UTC (rev 12096)
+++ trunk/packages/prank/trunk/debian/changelog 2012-08-20 14:41:22 UTC (rev 12097)
@@ -1,3 +1,15 @@
+prank (0.0.120716-1) precise; urgency=low
+
+ * Files now on Google Code - edited watchfile
+ * New upstream release
+ * Code is now in src/ subdirectory
+ * manpage patch has been incorporated in upstream, and I've added
+ the cleanup fixes into /debian/rules, so there are now no patches
+ * Prevent DH from doing QMake rebuild - see README.source for a
+ justification
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Mon, 20 Aug 2012 15:29:45 +0100
+
prank (0.0.111130-1) UNRELEASED; urgency=low
* Initial release. (Closes: #627391)
Modified: trunk/packages/prank/trunk/debian/control
===================================================================
--- trunk/packages/prank/trunk/debian/control 2012-08-20 13:40:51 UTC (rev 12096)
+++ trunk/packages/prank/trunk/debian/control 2012-08-20 14:41:22 UTC (rev 12097)
@@ -4,7 +4,7 @@
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
+Standards-Version: 3.9.3
Homepage: http://www.ebi.ac.uk/goldman-srv/prank/
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/prank/trunk/
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/prank/trunk/
Modified: trunk/packages/prank/trunk/debian/copyright
===================================================================
--- trunk/packages/prank/trunk/debian/copyright 2012-08-20 13:40:51 UTC (rev 12096)
+++ trunk/packages/prank/trunk/debian/copyright 2012-08-20 14:41:22 UTC (rev 12097)
@@ -5,12 +5,13 @@
Files: *
Copyright: © 2005-2011 Ari Loytynoja
License: GPL-v3
+ See: /usr/share/common-licenses/GPL-3
Files: debian/*
Copyright: © 2011 Manuel Prinz <manuel at debian.org>
License: GPL-v3
-Files: eigen.{h,cpp}
+Files: eigen.*
Copyright: © 2001 Ziheng Yang
License:
These files are copies from the PAML software package. The homepage
@@ -19,4 +20,3 @@
PAML is a package of programs for phylogenetic analyses of DNA or
protein sequences using maximum likelihood. It is maintained and
distributed for academic use free of charge by Ziheng Yang.
-
Deleted: trunk/packages/prank/trunk/debian/patches/fix-broken-clean-target.patch
===================================================================
--- trunk/packages/prank/trunk/debian/patches/fix-broken-clean-target.patch 2012-08-20 13:40:51 UTC (rev 12096)
+++ trunk/packages/prank/trunk/debian/patches/fix-broken-clean-target.patch 2012-08-20 14:41:22 UTC (rev 12097)
@@ -1,19 +0,0 @@
-Description: Small Makefile bugfixes
- This patch fixes a syntactic error in the Makefile and removes the compiled
- binary when the clean target is called.
-Author: Manuel Prinz <manuel at debian.org>
-Last-Update: 2011-05-20
---- 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
-
Deleted: trunk/packages/prank/trunk/debian/patches/manpage-for-prank.patch
===================================================================
--- trunk/packages/prank/trunk/debian/patches/manpage-for-prank.patch 2012-08-20 13:40:51 UTC (rev 12096)
+++ trunk/packages/prank/trunk/debian/patches/manpage-for-prank.patch 2012-08-20 14:41:22 UTC (rev 12097)
@@ -1,209 +0,0 @@
-Description: Add a man page for prank
- This patch adds a man page in POD format. The Makefile is updated to build the
- manpage and remove it in the clean target.
-Author: Manuel Prinz <manuel at debian.org>
-Last-Update: 2011-05-20
---- 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
Deleted: trunk/packages/prank/trunk/debian/patches/series
===================================================================
--- trunk/packages/prank/trunk/debian/patches/series 2012-08-20 13:40:51 UTC (rev 12096)
+++ trunk/packages/prank/trunk/debian/patches/series 2012-08-20 14:41:22 UTC (rev 12097)
@@ -1,2 +0,0 @@
-fix-broken-clean-target.patch
-manpage-for-prank.patch
Deleted: trunk/packages/prank/trunk/debian/prank.install
===================================================================
--- trunk/packages/prank/trunk/debian/prank.install 2012-08-20 13:40:51 UTC (rev 12096)
+++ trunk/packages/prank/trunk/debian/prank.install 2012-08-20 14:41:22 UTC (rev 12097)
@@ -1 +0,0 @@
-prank usr/bin/
Deleted: trunk/packages/prank/trunk/debian/prank.manpages
===================================================================
--- trunk/packages/prank/trunk/debian/prank.manpages 2012-08-20 13:40:51 UTC (rev 12096)
+++ trunk/packages/prank/trunk/debian/prank.manpages 2012-08-20 14:41:22 UTC (rev 12097)
@@ -1 +0,0 @@
-prank.1
Modified: trunk/packages/prank/trunk/debian/rules
===================================================================
--- trunk/packages/prank/trunk/debian/rules 2012-08-20 13:40:51 UTC (rev 12096)
+++ trunk/packages/prank/trunk/debian/rules 2012-08-20 14:41:22 UTC (rev 12097)
@@ -1,4 +1,18 @@
#!/usr/bin/make -f
+SRCDIR=src
+
%:
- dh $@
+ dh $@ --sourcedirectory=$(SRCDIR) --parallel
+
+override_dh_auto_clean:
+ # No distclean! See README.source
+ ( cd $(SRCDIR) ; make clean )
+ ( cd $(SRCDIR) ; rm -f prank prank.1 )
+
+override_dh_auto_build:
+ dh_auto_build --verbose
+
+override_dh_install:
+ dh_install $(SRCDIR)/prank /usr/bin
+ dh_installman $(SRCDIR)/prank.1
Modified: trunk/packages/prank/trunk/debian/watch
===================================================================
--- trunk/packages/prank/trunk/debian/watch 2012-08-20 13:40:51 UTC (rev 12096)
+++ trunk/packages/prank/trunk/debian/watch 2012-08-20 14:41:22 UTC (rev 12097)
@@ -1,2 +1,3 @@
version=3
-http://www.ebi.ac.uk/goldman-srv/prank/src/prank/prank\.src\.(\d{6})\.tgz
+opts="uversionmangle=s/^/0.0./" \
+http://code.google.com/p/prank-msa/downloads/list .*/files/prank\.src\.(\d{6})\.tgz
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