[med-svn] [gwama] 04/04: Initial debian/
Dylan Aïssi
bob.dybian-guest at moszumanska.debian.org
Wed Nov 19 08:15:49 UTC 2014
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 <bob.dybian at gmail.com>
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 <bob.dybian at gmail.com>,
+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 <bob.dybian at gmail.com> 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 <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Dylan Aïssi <bob.dybian at gmail.com>
+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 <bob.dybian at gmail.com>
+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 <bob.dybian at gmail.com>
+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
--
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