[med-svn] [roadtrips] 02/02: Initial Debian packaging
Andreas Tille
tille at debian.org
Fri Nov 20 14:53:05 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository roadtrips.
commit e53b5db4441972220566247f11a163dcd53d9830
Author: Andreas Tille <tille at debian.org>
Date: Fri Nov 20 15:46:03 2015 +0100
Initial Debian packaging
---
debian/README.Debian | 9 ++++++
debian/changelog | 5 ++++
debian/compat | 1 +
debian/control | 33 ++++++++++++++++++++++
debian/copyright | 44 ++++++++++++++++++++++++++++++
debian/install | 4 +++
debian/patches/debian_file_locations.patch | 23 ++++++++++++++++
debian/patches/hardening.patch | 15 ++++++++++
debian/patches/series | 2 ++
debian/rules | 16 +++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 11 ++++++++
debian/watch | 4 +++
13 files changed, 168 insertions(+)
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..90363f5
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,9 @@
+roadtrips for Debian
+====================
+
+Since the PDF documentation came without source it was removed from
+the upstream download archive. You can find the PDF online here:
+
+ http://faculty.washington.edu/tathornt/software/ROADTRIPS2/ROADTRIPS2_Documentation.pdf
+
+ -- Andreas Tille <tille at debian.org> Fri, 20 Nov 2015 14:29:17 +0100
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..441bb06
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+roadtrips (2.0+dfsg-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Fri, 20 Nov 2015 14:29:17 +0100
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..3a2d6cf
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,33 @@
+Source: roadtrips
+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: 3.9.6
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/roadtrips.git
+Vcs-Git: git://anonscm.debian.org/debian-med/roadtrips.git
+Homepage: http://faculty.washington.edu/tathornt/software/ROADTRIPS2/
+
+Package: roadtrips
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: case-control association testing with unknown population and pedigree structure
+ ROADTRIPS performs single-SNP, case-control association testing in
+ samples with partially or completely unknown population and pedigree
+ structure. ROADTRIPS uses an empirical covariance matrix calculated from
+ genomewide SNP data to correct for unknown population and pedigree
+ structure, while maintaining high power by taking advantage of known
+ pedigree information when it is available. The program is applicable to
+ association studies with completely general combinations of related and
+ unrelated individuals. Analysis can be performed genomewide (currently
+ just for autosomes).
+ .
+ ROADTRIPS is suitable for applications such as:
+ * correcting for possible population structure and/or misspecified
+ relationships in the context of case-control association testing in
+ samples of unrelated individuals and/or related individuals with well-
+ characterized pedigrees
+ * case-control association testing in samples from isolated populations
+ for which pedigree information is limited or unavailable
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..af82449
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,44 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: ROADTRIPS
+Source: http://faculty.washington.edu/tathornt/software/ROADTRIPS2/download.html
+Files-Excluded: */ROADTRIPS
+ *.pdf
+ ._*
+
+Files: *
+Copyright: 2010-2012 Timothy Thornton, Mary Sara McPeek
+License: GPL-3+
+
+Files: pnorms2.c
+Copyright: 1995, 1996 Robert Gentleman and Ross Ihaka
+License: GPL-2+
+ This program 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 program 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.
+ .
+ On Debian systems you can find the full text of the GNU General Public
+ License version 2 at /usr/share/common-licenses/GPL-2.
+
+Files: debian/*
+Copyright: 2015 Andreas Tille <tille at debian.org>
+License: GPL-3+
+
+License: GPL-3+
+ This program 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 3 of the License, or
+ (at your option) any later version.
+ .
+ This program 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.
+ .
+ On Debian systems you can find the full text of the GNU General Public
+ License at /usr/share/common-licenses/GPL.
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..602009b
--- /dev/null
+++ b/debian/install
@@ -0,0 +1,4 @@
+phenofile usr/share/roadtrips
+genofile usr/share/roadtrips
+kinfile usr/share/roadtrips
+prevalence usr/share/roadtrips
diff --git a/debian/patches/debian_file_locations.patch b/debian/patches/debian_file_locations.patch
new file mode 100644
index 0000000..47dd103
--- /dev/null
+++ b/debian/patches/debian_file_locations.patch
@@ -0,0 +1,23 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 20 Nov 2015 14:29:17 +0100
+Description: Debian installs the data files in /usr/share/roadtrip
+
+--- a/ROADTRIPS_SOURCE.c
++++ b/ROADTRIPS_SOURCE.c
+@@ -150,12 +150,12 @@ int main (int argc, char *argv[])
+ int mycount,numtyped,pers1,pers2,oldnumtyped,nonpolycount=0;
+ char tempname[100];
+ char str1[MAXLEN];
+- char pedfile[MAXLEN] = "phenofile";
+- char kinshipfile[MAXLEN] = "kinfile";
+- char prevfile[MAXLEN] = "prevalence";
++ char pedfile[MAXLEN] = "/usr/share/roadtrips/phenofile";
++ char kinshipfile[MAXLEN] = "/usr/share/roadtrips/kinfile";
++ char prevfile[MAXLEN] = "/usr/share/roadtrips/prevalence";
+ char samplefile[MAXLEN] = "study.sample";
+ char output[MAXLEN] = "output";
+- char typedfile[MAXLEN]="genofile";
++ char typedfile[MAXLEN]="/usr/share/roadtrips/genofile";
+ char input[MAXLEN];
+ char controlfile[MAXLEN];
+ char markerfile[MAXLEN];
diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch
new file mode 100644
index 0000000..1a4e31f
--- /dev/null
+++ b/debian/patches/hardening.patch
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 20 Nov 2015 14:29:17 +0100
+Description: Propagate hardening options
+
+--- a/Makefile
++++ b/Makefile
+@@ -22,7 +22,7 @@ OPTIONS = -O3
+ CC_LIB = -lm
+
+ ROADTRIPS: ROADTRIPS_SOURCE.c cholesky.c pnorms2.c nrutil.c nrutil.h
+- $(COMPILER) $(CC_LIB) $(OPTIONS) ROADTRIPS_SOURCE.c -o ROADTRIPS
++ $(COMPILER) $(CFLAGS) $(CC_LIB) $(OPTIONS) $(LDFLAGS) ROADTRIPS_SOURCE.c -o ROADTRIPS
+
+
+
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..b03df3b
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+debian_file_locations.patch
+hardening.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..d0d957e
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,16 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+
+%:
+ dh $@
+
+override_dh_install:
+ dh_install
+ mkdir -p debian/$(DEBPKGNAME)/usr/bin
+ cp -a ROADTRIPS debian/$(DEBPKGNAME)/usr/bin/roadtrips
+
+get-orig-source:
+ uscan --verbose --force-download --repack --compression xz
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..7d724f5
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,11 @@
+Reference:
+ Author: Timothy Thornton and Mary Sara McPeek
+ Title: "ROADTRIPS: Case-Control Association Testing with Partially or Completely Unknown Population and Pedigree Structure"
+ Journal: American Journal of Human Genetics
+ Year: 2010
+ Volume: 86
+ Number: 2
+ Pages: 172–184
+ DOI: 10.1016/j.ajhg.2010.01.001
+ PMID: 20137780
+ URL: http://www.sciencedirect.com/science/article/pii/S0002929710000029
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..0758967
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g" \
+ http://faculty.washington.edu/tathornt/software/ROADTRIPS2/download.html ROADTRIPS([\d.]+)\.tar\.gz
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/roadtrips.git
More information about the debian-med-commit
mailing list