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