[med-svn] [phipack] 02/02: Add initial packaging
Andreas Tille
tille at debian.org
Wed Apr 20 06:52:48 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository phipack.
commit a973ee17fad3f6019424e9afee0ffcca9c978e1f
Author: Andreas Tille <tille at debian.org>
Date: Wed Apr 20 08:51:55 2016 +0200
Add initial packaging
---
debian/README.Debian | 4 +++
debian/changelog | 5 ++++
debian/clean | 4 +++
debian/compat | 1 +
debian/control | 22 ++++++++++++++++
debian/copyright | 13 ++++++++++
debian/install | 3 +++
debian/links | 3 +++
debian/patches/fix_build_error.patch | 24 ++++++++++++++++++
debian/patches/hardening.patch | 49 ++++++++++++++++++++++++++++++++++++
debian/patches/series | 2 ++
debian/rules | 9 +++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 +++++++++
debian/watch | 7 ++++++
15 files changed, 159 insertions(+)
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..94785bc
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,4 @@
+For documentation please see
+
+ http://www.maths.otago.ac.nz/~dbryant/software/phimanual.pdf
+
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..b5745b0
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+phipack (0.0.20060425-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Tue, 19 Apr 2016 16:04:13 +0200
diff --git a/debian/clean b/debian/clean
new file mode 100644
index 0000000..80b768d
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1,4 @@
+Phi
+Profile
+ppma_2_bmp
+src/ppma_2_bmp/ppma_2_bmp
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..c50f260
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,22 @@
+Source: phipack
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/phipack.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/phipack.git
+Homepage: http://www.maths.otago.ac.nz/~dbryant/software/phimanual.pdf
+
+Package: phipack
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: PHI test and other tests of recombination
+ The PhiPack software package implements a few tests for recombination
+ and can produce refined incompatibility matrices as well. Specifically,
+ PHIPack implements the 'Pairwise Homoplasy Index', Maximum Chi2 and the
+ 'Neighbour Similarity Score'. The program Phi can be run to produce a
+ p-value of recombination within a data set and the program profile can
+ be run to determine regions exhibiting strongest evidence mosaicism.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..a22fa58
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,13 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: PhiPack
+Upstream-Contact: Trevor Bruen <tbruen at gmail.com>
+Source: http://www.maths.otago.ac.nz/~dbryant/software/PhiPack.tar
+
+Files: *
+Copyright: 2004-2006 Trevor Bruen <tbruen at gmail.com>, D. Bryant
+License: to_be_clarified
+ E-Mail contact is established to attach a proper license
+
+Files: debian/*
+Copyright: 2016 Andreas Tille <tille at debian.org>
+License: GPL-3+
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..73bebab
--- /dev/null
+++ b/debian/install
@@ -0,0 +1,3 @@
+Phi usr/lib/debian-med/bin
+Profile usr/lib/debian-med/bin
+ppma_2_bmp usr/lib/debian-med/bin
\ No newline at end of file
diff --git a/debian/links b/debian/links
new file mode 100644
index 0000000..d15b6b4
--- /dev/null
+++ b/debian/links
@@ -0,0 +1,3 @@
+usr/lib/debian-med/bin/Phi usr/bin/phipack-phi
+usr/lib/debian-med/bin/Profile usr/bin/phipack-profile
+usr/lib/debian-med/bin/ppma_2_bmp usr/bin/phipack-ppma_2_bmp
diff --git a/debian/patches/fix_build_error.patch b/debian/patches/fix_build_error.patch
new file mode 100644
index 0000000..7d6dd20
--- /dev/null
+++ b/debian/patches/fix_build_error.patch
@@ -0,0 +1,24 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 19 Apr 2016 16:04:13 +0200
+Description: Fix compilation with modern g++
+
+--- a/src/ppma_2_bmp/ppma_io.C
++++ b/src/ppma_2_bmp/ppma_io.C
+@@ -4,6 +4,7 @@
+ # include <fstream>
+ # include <cmath>
+ # include <ctime>
++# include <cstring>
+
+ using namespace std;
+
+--- a/src/ppma_2_bmp/ppma_2_bmp.C
++++ b/src/ppma_2_bmp/ppma_2_bmp.C
+@@ -3,6 +3,7 @@
+ # include <iomanip>
+ # include <fstream>
+ # include <ctime>
++# include <cstring>
+
+ using namespace std;
+
diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch
new file mode 100644
index 0000000..900c1fa
--- /dev/null
+++ b/debian/patches/hardening.patch
@@ -0,0 +1,49 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 19 Apr 2016 16:04:13 +0200
+Description: Propagate hardening options
+
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -1,7 +1,7 @@
+ # compiler
+ #CXX = /opt/ibmcmp/vac/6.0/bin/xlc
+ CXX = gcc
+-CXXFLAGS = -O3 -Wall
++CXXFLAGS += -O3 -Wall
+
+ # target macros
+ PhiOBJ = normal.o stats.o maxChi.o main.o queue.o graphCode.o fasta.o phylip.o mem.o misc.o pairScore.o seqManip.o global.o
+@@ -16,14 +16,14 @@ default : Phi Profile
+
+
+ Phi: $(PhiOBJ)
+- $(CXX) $(CXXFLAGS) -o Phi $(PhiOBJ) -lm
++ $(CXX) $(CXXFLAGS) -o Phi $(PhiOBJ) -lm $(LDFLAGS)
+ cp Phi ../
+ cd ppma_2_bmp && ${MAKE}
+ cp ppma_2_bmp/ppma_2_bmp ../
+
+
+ Profile: $(ProfOBJ)
+- $(CXX) $(CXXFLAGS) -o Profile $(ProfOBJ) -lm $(MYLIB)
++ $(CXX) $(CXXFLAGS) -o Profile $(ProfOBJ) -lm $(MYLIB) $(LDFLAGS)
+ cp Profile ../
+ clean : FORCE
+ rm -f *.o
+--- a/src/ppma_2_bmp/Makefile
++++ b/src/ppma_2_bmp/Makefile
+@@ -1,12 +1,12 @@
+ # compiler
+ CXX = g++
+-CXXFLAGS = -O3
++CXXFLAGS += -O3
+
+ # targets
+ default : ppma_2_bmp
+
+ ppma_2_bmp:
+- $(CXX) $(CXXFLAGS) -o ppma_2_bmp ppma_io.C bmp_io.C ppma_2_bmp.C -lm
++ $(CXX) $(CXXFLAGS) -o ppma_2_bmp ppma_io.C bmp_io.C ppma_2_bmp.C -lm $(LDFLAGS)
+
+ clean : FORCE
+ rm -f *.o
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..f59d1c0
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+hardening.patch
+fix_build_error.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..64e8665
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,9 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+
+%:
+ dh $@ --sourcedirectory=src
+
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..f02c597
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Trevor C. Bruen and Hervé Philippe and David Bryant
+ Title: A Simple and Robust Statistical Test for Detecting the Presence of Recombination
+ Journal: Genetics
+ Year: 2006
+ Volume: 172
+ Number: 4
+ Pages: 2665-2681
+ DOI: 10.1534/genetics.105.048975
+ PMID: 16489234
+ URL: http://www.genetics.org/content/172/4/2665
+ eprint: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1456386/pdf/GEN17242665.pdf
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..e521044
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,7 @@
+#The only trace for this program in the internet that has been found
+#was
+#
+# http://www.maths.otago.ac.nz/~dbryant/software/PhiPack.tar
+#
+#The authors are contacted and will provide some better means for
+#versioned download.
--
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