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commit a973ee17fad3f6019424e9afee0ffcca9c978e1f Author: Andreas Tille <[email protected]> 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 <[email protected]> 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 <[email protected]> +Uploaders: Andreas Tille <[email protected]> +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 <[email protected]> +Source: http://www.maths.otago.ac.nz/~dbryant/software/PhiPack.tar + +Files: * +Copyright: 2004-2006 Trevor Bruen <[email protected]>, D. Bryant +License: to_be_clarified + E-Mail contact is established to attach a proper license + +Files: debian/* +Copyright: 2016 Andreas Tille <[email protected]> +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 <[email protected]> +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 <[email protected]> +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. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/phipack.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
