This is an automated email from the git hooks/post-receive script. bob.dybian-guest pushed a commit to branch master in repository gwama.
commit 7cabb42380de022910d57462b8df9634e26521eb Author: Dylan Aïssi <[email protected]> Date: Wed Nov 19 08:55:28 2014 +0100 Initial debian/ --- debian/GWAMA.1 | 103 +++++++++++++++++++++ debian/TODO.Debian | 7 ++ debian/changelog | 5 + debian/compat | 1 + debian/control | 27 ++++++ debian/copyright | 54 +++++++++++ debian/gwama.install | 1 + debian/manpages | 1 + ..._Makefile_Add_FLAGS_to_activate_Hardening.patch | 15 +++ debian/patches/series | 1 + debian/rules | 17 ++++ debian/source/format | 1 + debian/upstream/metadata | 24 +++++ debian/watch | 2 + 14 files changed, 259 insertions(+) diff --git a/debian/GWAMA.1 b/debian/GWAMA.1 new file mode 100644 index 0000000..a88cbc7 --- /dev/null +++ b/debian/GWAMA.1 @@ -0,0 +1,103 @@ +.\" +.TH GWAMA 1 "November 2014" "2.1" +.SH NAME +GWAMA \- Genome-Wide Association Meta Analysis +.SH SYNOPSIS +.B GWAMA +[\fIoptions\fR] +.SH DESCRIPTION +GWAMA (Genome-Wide Association Meta Analysis) software performs +meta-analysis of the results of GWA studies of binary or +quantitative phenotypes. Fixed- and random-effect meta-analyses are +performed for both directly genotyped and imputed SNPs using +estimates of the allelic odds ratio and 95% confidence interval for +binary traits, and estimates of the allelic effect size and standard +error for quantitative phenotypes. GWAMA can be used for analysing +the results of all different genetic models (multiplicative, +additive, dominant, recessive). The software incorporates error +trapping facilities to identify strand alignment errors and allele +flipping, and performs tests of heterogeneity of effects between studies. +.SH OPTIONS +.TP +\fB\-i\fR, \fB\-\-filelist\fR=\fIfilename\fR +Specify studies' result files. Default = gwama.in +.TP +\fB\-o\fR, \fB\-\-output\fR=\fIfileroot\fR +Specify file root for output of analysis. Default = gwama (gwama.out, gwama.gc.out) +.TP +\fB\-r\fR, \fB\-\-random\fR +Use random effect correction. Default = disabled +.TP +\fB\-gc\fR, \fB\-\-genomic_control\fR +Use genomic control for adjusting studies' result files. Default = disabled +.TP +\fB\-gco\fR, \fB\-\-genomic_control_output\fR +Use genomic control on meta-analysis summary (i.e. results of meta- analysis are corrected for gc). Default = disabled +.TP +\fB\-qt\fR, \fB\-\-quantitative\fR +Select quantitative trait version (BETA and SE columns). Default = binary trait +.TP +\fB\-m\fR, \fB\-\-map\fR=\fIfilename\fR +Select file name for marker map. +.TP +\fB\-t\fR, \fB\-\-threshold\fR=\fI0-1\fR +The p-value threshold for showing direction in summary effect directions. Default = 1 +.TP +\fB\-\-no_alleles\fR +No allele information has been given. Expecting always the same EA. +.TP +\fB\-\-indel_alleles\fR +Allele labes might contain more than single letter. No strand checks. +.TP +\fB\-\-sex\fR +Run gender-differentiated and gender- heterogeneity analysis (method described in paper Magi, Lindgren & Morris 2010). Gender info must be provided in filelist file. (second column after file names is either M or F). +.TP +\fB\-\-name_marker\fR +Alternative header to marker name col. +.TP +\fB\-\-name_strand\fR +Alternative header to strand column. +.TP +\fB\-\-name_n\fR +Alternative header to sample size col. +.TP +\fB\-\-name_ea\fR +Alternative header to effect allele column. +.TP +\fB\-\-name_nea\fR +Alternative header to non-effect allele column. +.TP +\fB\-\-name_eaf\fR +Alternative header to effect allele frequency column. +.TP +\fB\-\-name_beta\fR +Alternative header to beta column. +.TP +\fB\-\-name_se\fR +Alternative header to std. err. col. +.TP +\fB\-\-name_or\fR +Alternative header to OR column. +.TP +\fB\-\-name_or_95l\fR +Alternative header to OR 95L column. +.TP +\fB\-\-name_or_95u\fR +Alternative header to OR 95U column. +.TP +\fB\-h\fR, \fB\-\-help\fR +Print this help. +.TP +\fB\-v\fR, \fB\-\-version\fR +Print GWAMA version number. +This manual page must be insufficient. Please use the help option for a +quick reminder of the options of gwama or turn to its home page with +the online documentation or the downloadable manual. +.SH SEE ALSO +.BR http://www.well.ox.ac.uk/gwama/ +.SH AUTHOR +GWAMA was written by Reedik Magi and Andrew P Morris. +.PP +This manual page was written by Dylan Aïssi <[email protected]>, +for the Debian project (but may be used by others). + diff --git a/debian/TODO.Debian b/debian/TODO.Debian new file mode 100644 index 0000000..4fc2d09 --- /dev/null +++ b/debian/TODO.Debian @@ -0,0 +1,7 @@ +# Remove __MACOSX upstream folder + +# Add addtional files from http://www.well.ox.ac.uk/gwama/download.shtml +# -- Changelog - http://www.well.ox.ac.uk/gwama/log2.txt +# -- Samples files - http://www.well.ox.ac.uk/gwama/samples.zip +# -- R scritps - http://www.well.ox.ac.uk/gwama/*.R +# -- Perl scritps - http://www.well.ox.ac.uk/gwama/*.pl diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..545f5b2 --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +gwama (2.1-1) UNRELEASED; urgency=low + + * Initial Debian Release. (Closes: #770143) + + -- Dylan Aïssi <[email protected]> Wed, 19 Nov 2014 07:39:06 +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..b0cffcd --- /dev/null +++ b/debian/control @@ -0,0 +1,27 @@ +Source: gwama +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Dylan Aïssi <[email protected]> +Build-Depends: debhelper (>= 9), + zlib1g-dev +Standards-Version: 3.9.6 +Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/gwama.git +Vcs-Git: git://anonscm.debian.org/debian-med/gwama.git +Homepage: http://www.well.ox.ac.uk/gwama/ + +Package: gwama +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: Genome-Wide Association Meta Analysis + GWAMA (Genome-Wide Association Meta Analysis) software performs + meta-analysis of the results of GWA studies of binary or + quantitative phenotypes. Fixed- and random-effect meta-analyses are + performed for both directly genotyped and imputed SNPs using + estimates of the allelic odds ratio and 95% confidence interval for + binary traits, and estimates of the allelic effect size and standard + error for quantitative phenotypes. GWAMA can be used for analysing + the results of all different genetic models (multiplicative, + additive, dominant, recessive). The software incorporates error + trapping facilities to identify strand alignment errors and allele + flipping, and performs tests of heterogeneity of effects between studies. diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..38922c2 --- /dev/null +++ b/debian/copyright @@ -0,0 +1,54 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: GWAMA +Upstream-Contact: Reedik Mägi <reedik at well.ox.ac.uk> +Source: http://www.well.ox.ac.uk/gwama/ + +Files: * +Copyright: 2009-2010 Reedik Mägi, Andrew P Morris. +License: BSD-3-clause + +Files: ap.* apvt.h +Copyright: 2003-2008 Sergey Bochkanov (ALGLIB project). +License: BSD-3-clause + +Files: chisquaredistr.* gammaf.* igammaf.* normaldistr.* +Copyright: 1984-2007 Stephen L. Moshier, Sergey Bochkanov (ALGLIB project). +License: BSD-3-clause + +Files: statistics.* +Copyright: 2002-2003 Reedik Mägi, Lauris Kaplinski, BioData, Ltd. +License: BSD-3-clause + +Files: debian/* +Copyright: 2014 Dylan Aïssi <[email protected]> +License: BSD-3-clause + +License: BSD-3-clause + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions are + met: + . + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + . + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer listed + in this license in the documentation and/or other materials + provided with the distribution. + . + 3. Neither the name of the copyright holders nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + . + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT + LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR + A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT + OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, + DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY + THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE + OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + diff --git a/debian/gwama.install b/debian/gwama.install new file mode 100644 index 0000000..d0a9276 --- /dev/null +++ b/debian/gwama.install @@ -0,0 +1 @@ +GWAMA usr/bin/ diff --git a/debian/manpages b/debian/manpages new file mode 100644 index 0000000..71c2fbf --- /dev/null +++ b/debian/manpages @@ -0,0 +1 @@ +debian/GWAMA.1 diff --git a/debian/patches/01_Makefile_Add_FLAGS_to_activate_Hardening.patch b/debian/patches/01_Makefile_Add_FLAGS_to_activate_Hardening.patch new file mode 100644 index 0000000..d848147 --- /dev/null +++ b/debian/patches/01_Makefile_Add_FLAGS_to_activate_Hardening.patch @@ -0,0 +1,15 @@ +Author: Dylan Aïssi <[email protected]> +Description: Add FLAGS to Makefile to activate Hardening +Forwarded: not-needed +Last-Update: 2014-11-19 + +--- a/Makefile ++++ b/Makefile +@@ -8,5 +8,5 @@ + + GWAMA: main.cpp + +- g++ main.cpp marker.cpp statistics.cpp study.cpp chisquaredistr.cpp normaldistr.cpp gammaf.cpp igammaf.cpp ap.cpp global.cpp problem.cpp tools.cpp cohort.cpp commandLine.cpp readFile.cpp $(DEBUGFLAGS) -o GWAMA ++ g++ $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) main.cpp marker.cpp statistics.cpp study.cpp chisquaredistr.cpp normaldistr.cpp gammaf.cpp igammaf.cpp ap.cpp global.cpp problem.cpp tools.cpp cohort.cpp commandLine.cpp readFile.cpp $(DEBUGFLAGS) -o GWAMA + + diff --git a/debian/patches/series b/debian/patches/series new file mode 100644 index 0000000..d130fac --- /dev/null +++ b/debian/patches/series @@ -0,0 +1 @@ +01_Makefile_Add_FLAGS_to_activate_Hardening.patch diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..3db83ea --- /dev/null +++ b/debian/rules @@ -0,0 +1,17 @@ +#!/usr/bin/make -f +# -*- makefile -*- +# debian/rules file for the Debian/GNU Linux gwama package + +# Don't override the upstream FLAG -O3 +CXXFLAGS=$(shell dpkg-buildflags --get CXXFLAGS 2>/dev/null | sed -e 's/-O2//g') + +%: + dh $@ + +override_dh_auto_build: + # Don't override the upstream FLAG -O3 + make CXXFLAGS="$(CXXFLAGS)" + +get-orig-source: + uscan --verbose --force-download --repack --compress 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..d7c7ff7 --- /dev/null +++ b/debian/upstream/metadata @@ -0,0 +1,24 @@ +Contact: Reedik Mägi <reedik at well.ox.ac.uk> +Name: Gwama +Reference: + Author: Reedik Mägi and Andrew P. Morris + Title: "GWAMA: software for genome-wide association meta-analysis" + Journal: BMC Bioinformatics + Volume: 11 + Number: May + Pages: 288 + Year: 2010 + DOI: 10.1186/1471-2105-11-288 + URL: http://www.biomedcentral.com/1471-2105/11/288 + eprint: http://www.biomedcentral.com/content/pdf/1471-2105-11-288.pdf + + Author: Reedik Magi, Cecilia M. Lindgren and Andrew P. Morris + Title: "Meta-analysis of sex-specific genome-wide association studies" + Journal: Genetic Epidemiology + Volume: 34 + Number: 8 + Pages: 846-853 + Year: 2010 + DOI: 10.1002/gepi.20540 + URL: http://onlinelibrary.wiley.com/doi/10.1002/gepi.20540/full + eprint: http://onlinelibrary.wiley.com/doi/10.1002/gepi.20540/pdf diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..9260637 --- /dev/null +++ b/debian/watch @@ -0,0 +1,2 @@ +version=3 +http://www.well.ox.ac.uk/gwama/download.shtml gwama(\d\S*)\.zip -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/gwama.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
