[med-svn] r13911 - in trunk/packages: . emmax emmax/trunk emmax/trunk/debian emmax/trunk/debian/patches emmax/trunk/debian/source
Steffen Möller
moeller at alioth.debian.org
Tue Jun 11 09:09:19 UTC 2013
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 <moeller at debian.org> 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 <moeller at debian.org> 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 <moeller at debian.org>
+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 <moeller at debian.org>
+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)
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