Author: moeller Date: 2013-06-11 09:09:19 +0000 (Tue, 11 Jun 2013) New Revision: 13911
Added: trunk/packages/emmax/ trunk/packages/emmax/trunk/ trunk/packages/emmax/trunk/debian/ trunk/packages/emmax/trunk/debian/README.Debian trunk/packages/emmax/trunk/debian/README.source trunk/packages/emmax/trunk/debian/changelog trunk/packages/emmax/trunk/debian/compat trunk/packages/emmax/trunk/debian/control trunk/packages/emmax/trunk/debian/copyright trunk/packages/emmax/trunk/debian/emmax-kin.1 trunk/packages/emmax/trunk/debian/emmax.1 trunk/packages/emmax/trunk/debian/emmax.install trunk/packages/emmax/trunk/debian/manpages trunk/packages/emmax/trunk/debian/patches/ trunk/packages/emmax/trunk/debian/patches/aborts.patch trunk/packages/emmax/trunk/debian/patches/dynamic.patch trunk/packages/emmax/trunk/debian/patches/paths.patch trunk/packages/emmax/trunk/debian/patches/series trunk/packages/emmax/trunk/debian/rules trunk/packages/emmax/trunk/debian/source/ trunk/packages/emmax/trunk/debian/source/format Log: Found emmax source code (rather than following the easy route to the provided binaries) and compiled it. I do not feel like performing the last steps for an upload to the distribution ... and, hey, the package may be sufficiently prominent to attract a volunteer to our distribution. I happily help out with the sponsoring for anyone who completes the packaging. This would comprise * communicating with upstream about the license * improving descriptions * getting references to publication in http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3092069/ Thanks Steffen Added: trunk/packages/emmax/trunk/debian/README.Debian =================================================================== --- trunk/packages/emmax/trunk/debian/README.Debian (rev 0) +++ trunk/packages/emmax/trunk/debian/README.Debian 2013-06-11 09:09:19 UTC (rev 13911) @@ -0,0 +1,14 @@ +emmax for Debian +---------------- + +The packaging was performed to meet local demands. It is shared to +help any upcoming adopter to bring the package into a redistributable way. + +To reseed the man pages shipping with this package, perform +$ sudo apt-get install help2man +$ help2man -h "" -N -n emmax --no-discard-stderr ./emmax > debian/emmax.1 --no-discard-stderr ./emmax > debian/emmax.1 +$ help2man -h "" -N -n emmax-kin --no-discard-stderr ./emmax-kin > debian/emmax-kin.1 --no-discard-stderr ./emmax-kin > debian/emmax-kin.1 + +The package was not yet uploaded because of an unclarified situation with the license. Any volunteer to help out by communicating with upstream is much welcome to steam ahead. + + -- Steffen Moeller <[email protected]> Mon, 10 Jun 2013 13:26:24 +0200 Added: trunk/packages/emmax/trunk/debian/README.source =================================================================== --- trunk/packages/emmax/trunk/debian/README.source (rev 0) +++ trunk/packages/emmax/trunk/debian/README.source 2013-06-11 09:09:19 UTC (rev 13911) @@ -0,0 +1,7 @@ +emmax for Debian +---------------- + +This source tree is incomplete in the sense that it does not provide any +license information. With what is currently known about EMMAX, the source +remains undistribtable. + Added: trunk/packages/emmax/trunk/debian/changelog =================================================================== --- trunk/packages/emmax/trunk/debian/changelog (rev 0) +++ trunk/packages/emmax/trunk/debian/changelog 2013-06-11 09:09:19 UTC (rev 13911) @@ -0,0 +1,6 @@ +emmax (0~beta.20100307-1) UNRELEASED; urgency=low + + * Initial release pending, not uploaded because of unknown license. + * Created rough help2man-seeded man pages + + -- Steffen Moeller <[email protected]> Mon, 10 Jun 2013 13:26:24 +0200 Added: trunk/packages/emmax/trunk/debian/compat =================================================================== --- trunk/packages/emmax/trunk/debian/compat (rev 0) +++ trunk/packages/emmax/trunk/debian/compat 2013-06-11 09:09:19 UTC (rev 13911) @@ -0,0 +1 @@ +8 Added: trunk/packages/emmax/trunk/debian/control =================================================================== --- trunk/packages/emmax/trunk/debian/control (rev 0) +++ trunk/packages/emmax/trunk/debian/control 2013-06-11 09:09:19 UTC (rev 13911) @@ -0,0 +1,33 @@ +Source: emmax +Section: science +Priority: optional +Maintainer: Steffen Moeller <[email protected]> +Build-Depends: debhelper (>= 8.0.0), libatlas-dev +Standards-Version: 3.9.4 +Homepage: http://genome.sph.umich.edu/wiki/EMMAX +#Vcs-Git: git://git.debian.org/collab-maint/emmax.git +#Vcs-Browser: http://git.debian.org/?p=collab-maint/emmax.git;a=summary + +Package: emmax +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: genetic mapping considering population structure + EMMAX is a statistical test for large scale human or model organism + association mapping accounting for the sample structure. In addition + to the computational efficiency obtained by EMMA algorithm, EMMAX takes + advantage of the fact that each locus explains only a small fraction of + complex traits, which allows to avoid repetitive variance component + estimation procedure, resulting in a significant amount of increase in + computational time of association mapping using mixed model. + +Package: emmax-dbg +Architecture: any +Section: debug +Priority: extra +Depends: emmax (= ${binary:Version}), ${misc:Depends} +Description: debug information for emmax + This package contains the dubgging symbols for emmax. + In case of a reproducible crash, you may be asked by + the developers to install this package and provide + a better annotated backtrace. + Added: trunk/packages/emmax/trunk/debian/copyright =================================================================== --- trunk/packages/emmax/trunk/debian/copyright (rev 0) +++ trunk/packages/emmax/trunk/debian/copyright 2013-06-11 09:09:19 UTC (rev 13911) @@ -0,0 +1,31 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: emmax +Source: http://www.sph.umich.edu/csg/kang/emmax/download/index.html + +Files: * +Copyright: <years> <put author's name and email here> + <years> <likewise for another author> +License: unknown + <Put the license of the package here indented by 1 space> + <This follows the format of Description: lines in control file> + . + <Including paragraphs> + +Files: debian/* +Copyright: 2013 Steffen Moeller <[email protected]> +License: GPL-2+ + This package 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 package 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. + . + You should have received a copy of the GNU General Public License + along with this program. If not, see <http://www.gnu.org/licenses/> + . + On Debian systems, the complete text of the GNU General + Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". Added: trunk/packages/emmax/trunk/debian/emmax-kin.1 =================================================================== --- trunk/packages/emmax/trunk/debian/emmax-kin.1 (rev 0) +++ trunk/packages/emmax/trunk/debian/emmax-kin.1 2013-06-11 09:09:19 UTC (rev 13911) @@ -0,0 +1,22 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.43.2. +.TH EMMAX-KIN: "1" "June 2013" "emmax-kin: invalid option -- '-'" "User Commands" +.SH NAME +emmax-kin: \- emmax-kin +.SH SYNOPSIS +.B emmax-kin +[\fItpedf\fR] +.SH DESCRIPTION +Required parameters +.TP +[tpedf] +: tped file +.TP +[outf] +: output file name +.PP +Optional parameters +.TP +\fB\-d\fR [# digits] +: precision of the kinship values (default : 10) +.HP +\fB\-v\fR : turn on verbose mode Added: trunk/packages/emmax/trunk/debian/emmax.1 =================================================================== --- trunk/packages/emmax/trunk/debian/emmax.1 (rev 0) +++ trunk/packages/emmax/trunk/debian/emmax.1 2013-06-11 09:09:19 UTC (rev 13911) @@ -0,0 +1,68 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.43.2. +.TH EMMAX: "1" "June 2013" "emmax: invalid option -- '-'" "User Commands" +.SH NAME +emmax: \- emmax +.SH SYNOPSIS +.B emmax +[\fIoptions\fR] +.SH DESCRIPTION +Required parameters +.HP +\fB\-t\fR [tpedf_prefix] : prefix for tped/tfam files +.TP +\fB\-o\fR [out_prefix] +: output file name prefix +.PP +Likely essential parameters +.HP +\fB\-p\fR [phenof] : 3\-column phenotype file with FAMID, INDID at the first two colmns, in the same order of .tfam file. Not required only with \fB\-K\fR option \fB\-k\fR [kinf] : n * n matrix containing kinship values in the individual order consistent to [tpedf].tfam file. [tpedf].kinf will be used if not specified +.HP +\fB\-c\fR [covf] : multi\-column covariate file with FAMID, INDID at the first two colmns, in the same order of .tfam fileOptional parameters +.HP +\fB\-i\fR [in_prefix] : input file name prefix including eigenvectors +.TP +\fB\-d\fR [# digits] +: precision of the output values (default : 5) +.HP +\fB\-s\fR [start index of SNP] : start index of SNP (default : 0) +.HP +\fB\-e\fR [end index of SNP] : end index of SNP (default : #snps) +.HP +\fB\-w\fR : flag for writing eigenvalues/eigenvector files +.HP +\fB\-D\fR [delimiters] : delimter string in quotation marks +.HP +\fB\-P\fR [# heaer cols in tped] : # of column headers in tped file +.HP +\fB\-F\fR [# heaer cols in tfam] : # of column headers in tfam file +.PP +Error : Unknown option character ?Usage: emmax [options] +Required parameters +.HP +\fB\-t\fR [tpedf_prefix] : prefix for tped/tfam files +.TP +\fB\-o\fR [out_prefix] +: output file name prefix +.PP +Likely essential parameters +.HP +\fB\-p\fR [phenof] : 3\-column phenotype file with FAMID, INDID at the first two colmns, in the same order of .tfam file. Not required only with \fB\-K\fR option \fB\-k\fR [kinf] : n * n matrix containing kinship values in the individual order consistent to [tpedf].tfam file. [tpedf].kinf will be used if not specified +.HP +\fB\-c\fR [covf] : multi\-column covariate file with FAMID, INDID at the first two colmns, in the same order of .tfam fileOptional parameters +.HP +\fB\-i\fR [in_prefix] : input file name prefix including eigenvectors +.TP +\fB\-d\fR [# digits] +: precision of the output values (default : 5) +.HP +\fB\-s\fR [start index of SNP] : start index of SNP (default : 0) +.HP +\fB\-e\fR [end index of SNP] : end index of SNP (default : #snps) +.HP +\fB\-w\fR : flag for writing eigenvalues/eigenvector files +.HP +\fB\-D\fR [delimiters] : delimter string in quotation marks +.HP +\fB\-P\fR [# heaer cols in tped] : # of column headers in tped file +.HP +\fB\-F\fR [# heaer cols in tfam] : # of column headers in tfam file Added: trunk/packages/emmax/trunk/debian/emmax.install =================================================================== --- trunk/packages/emmax/trunk/debian/emmax.install (rev 0) +++ trunk/packages/emmax/trunk/debian/emmax.install 2013-06-11 09:09:19 UTC (rev 13911) @@ -0,0 +1,2 @@ +emmax +emmax-kin Added: trunk/packages/emmax/trunk/debian/manpages =================================================================== --- trunk/packages/emmax/trunk/debian/manpages (rev 0) +++ trunk/packages/emmax/trunk/debian/manpages 2013-06-11 09:09:19 UTC (rev 13911) @@ -0,0 +1,2 @@ +debian/emmax.1 +debian/emmax-kin.1 Added: trunk/packages/emmax/trunk/debian/patches/aborts.patch =================================================================== --- trunk/packages/emmax/trunk/debian/patches/aborts.patch (rev 0) +++ trunk/packages/emmax/trunk/debian/patches/aborts.patch 2013-06-11 09:09:19 UTC (rev 13911) @@ -0,0 +1,51 @@ +Index: emmax-0~beta.20100307/emmax-kin.c +=================================================================== +--- emmax-0~beta.20100307.orig/emmax-kin.c ++++ emmax-0~beta.20100307/emmax-kin.c +@@ -46,7 +46,7 @@ + FILE* readfile(char* filename); + + void print_help(void) { +- fprintf(stderr,"Usage: emmax_IBS_kin [tpedf]\n"); ++ fprintf(stderr,"Usage: emmax-kin [tpedf]\n"); + fprintf(stderr,"Required parameters\n"); + fprintf(stderr,"\t[tpedf] : tped file\n"); + fprintf(stderr,"\t[outf] : output file name\n"); +@@ -114,6 +114,12 @@ + } + } + ++ // With no options given, present help but do not abort. ++ if (1 == argc) { ++ print_help(); ++ exit(-1); ++ } ++ + if ( ( rand_fill_flag == 1 ) && ( hetero_division_flag == 1 ) ) { + emmax_error("-r and -h option cannot be combined"); + } +Index: emmax-0~beta.20100307/emmax.c +=================================================================== +--- emmax-0~beta.20100307.orig/emmax.c ++++ emmax-0~beta.20100307/emmax.c +@@ -200,6 +200,12 @@ + } + } + ++ if (1 == argc) { ++ // when called with no arguments, just some help is fine, a crash is not. ++ print_help(); ++ exit(-1); ++ } ++ + // Sanity check for the number of required parameters + if ( argc > optind ) { + print_help(); +@@ -1580,7 +1586,6 @@ + fprintf(stderr,"\t-k [kinf] : n * n matrix containing kinship values in the individual order consistent to [tpedf].tfam file. [tpedf].kinf will be used if not specified\n"); + fprintf(stderr,"\t-c [covf] : multi-column covariate file with FAMID, INDID at the first two colmns, in the same order of .tfam file"); + fprintf(stderr,"Optional parameters\n"); +- fprintf(stderr,"Optional parameters\n"); + fprintf(stderr,"\t-i [in_prefix] : input file name prefix including eigenvectors\n"); + fprintf(stderr,"\t-d [# digits] : precision of the output values (default : 5)\n"); + fprintf(stderr,"\t-s [start index of SNP] : start index of SNP (default : 0)\n"); Added: trunk/packages/emmax/trunk/debian/patches/dynamic.patch =================================================================== --- trunk/packages/emmax/trunk/debian/patches/dynamic.patch (rev 0) +++ trunk/packages/emmax/trunk/debian/patches/dynamic.patch 2013-06-11 09:09:19 UTC (rev 13911) @@ -0,0 +1,28 @@ +Index: emmax-0~beta.20100307/makefile +=================================================================== +--- emmax-0~beta.20100307.orig/makefile ++++ emmax-0~beta.20100307/makefile +@@ -1,20 +1,11 @@ + # HAPA makefile + +-MODE = + INCFLAGS = + LIBFLAGS = -Wall + +-ifeq ($(MODE),debug) +- #Debug flags +- COMPFLAGS = ${INCFLAGS} -g -Wall +- CC = gcc +- CLIBS = /usr/lib/atlas/liblapack.a /usr/lib/atlas/libblas.a /usr/lib/libatlas.a /usr/lib/libg2c.a /usr/lib/libcblas.a /usr/lib/libm.a /usr/lib/libz.a +-else +- #Efficient Flags +- COMPFLAGS = ${INCFLAGS} -O2 -Wall +- CC = gcc +- CLIBS = /usr/lib/atlas/liblapack.a /usr/lib/atlas/libblas.a /usr/lib/libatlas.a /usr/lib/libg2c.a /usr/lib/libcblas.a /usr/lib/libm.a /usr/lib/libz.a +-endif ++COMPFLAGS = ${INCFLAGS} -O2 -Wall -g ++CC = gcc ++CLIBS = -L/usr/lib/atlas-base -L/usr/lib/lapack/ -llapack_atlas -llapack -lcblas -lblas -latlas -lcblas -lm -lz + + all: emmax emmax-kin + Added: trunk/packages/emmax/trunk/debian/patches/paths.patch =================================================================== --- trunk/packages/emmax/trunk/debian/patches/paths.patch (rev 0) +++ trunk/packages/emmax/trunk/debian/patches/paths.patch 2013-06-11 09:09:19 UTC (rev 13911) @@ -0,0 +1,13 @@ +Index: emmax-0~beta.20100307/emmax.c +=================================================================== +--- emmax-0~beta.20100307.orig/emmax.c ++++ emmax-0~beta.20100307/emmax.c +@@ -7,7 +7,7 @@ + #include <float.h> + #include <time.h> + #include <cblas.h> +-#include <clapack.h> ++#include <atlas/clapack.h> + #include <zlib.h> + //#include "lapack_wrapper.h" + Added: trunk/packages/emmax/trunk/debian/patches/series =================================================================== --- trunk/packages/emmax/trunk/debian/patches/series (rev 0) +++ trunk/packages/emmax/trunk/debian/patches/series 2013-06-11 09:09:19 UTC (rev 13911) @@ -0,0 +1,3 @@ +dynamic.patch +paths.patch +aborts.patch Added: trunk/packages/emmax/trunk/debian/rules =================================================================== --- trunk/packages/emmax/trunk/debian/rules (rev 0) +++ trunk/packages/emmax/trunk/debian/rules 2013-06-11 09:09:19 UTC (rev 13911) @@ -0,0 +1,16 @@ +#!/usr/bin/make -f +# -*- makefile -*- +# Sample debian/rules that uses debhelper. +# This file was originally written by Joey Hess and Craig Small. +# As a special exception, when this file is copied by dh-make into a +# dh-make output file, you may use that output file without restriction. +# This special exception was added by Craig Small in version 0.37 of dh-make. + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +%: + dh $@ --parallel + +override_dh_strip: + dh_strip --dbg-package=emmax-dbg Property changes on: trunk/packages/emmax/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/emmax/trunk/debian/source/format =================================================================== --- trunk/packages/emmax/trunk/debian/source/format (rev 0) +++ trunk/packages/emmax/trunk/debian/source/format 2013-06-11 09:09:19 UTC (rev 13911) @@ -0,0 +1 @@ +3.0 (quilt) _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
