[med-svn] r1477 - in trunk/packages: . loki loki/trunk loki/trunk/debian
tille at alioth.debian.org
tille at alioth.debian.org
Tue Feb 26 20:17:23 UTC 2008
Author: tille
Date: 2008-02-26 20:17:22 +0000 (Tue, 26 Feb 2008)
New Revision: 1477
Added:
trunk/packages/loki/
trunk/packages/loki/trunk/
trunk/packages/loki/trunk/debian/
trunk/packages/loki/trunk/debian/README.Debian
trunk/packages/loki/trunk/debian/changelog
trunk/packages/loki/trunk/debian/check_het.1
trunk/packages/loki/trunk/debian/compat
trunk/packages/loki/trunk/debian/control
trunk/packages/loki/trunk/debian/copyright
trunk/packages/loki/trunk/debian/hist.1
trunk/packages/loki/trunk/debian/loki-doc.README.Debian
trunk/packages/loki/trunk/debian/loki-doc.doc-base.lokifaq
trunk/packages/loki/trunk/debian/loki-doc.doc-base.lokimanual
trunk/packages/loki/trunk/debian/loki-doc.docs
trunk/packages/loki/trunk/debian/loki.1
trunk/packages/loki/trunk/debian/loki.dirs
trunk/packages/loki/trunk/debian/loki.docs
trunk/packages/loki/trunk/debian/loki_count.1
trunk/packages/loki/trunk/debian/loki_dist.1
trunk/packages/loki/trunk/debian/loki_ext.1
trunk/packages/loki/trunk/debian/loki_freq.1
trunk/packages/loki/trunk/debian/loki_sort_error.1
trunk/packages/loki/trunk/debian/menu
trunk/packages/loki/trunk/debian/prep.1
trunk/packages/loki/trunk/debian/qavg.1
trunk/packages/loki/trunk/debian/rules
trunk/packages/loki/trunk/debian/watch
Log:
put loki under version control
Added: trunk/packages/loki/trunk/debian/README.Debian
===================================================================
--- trunk/packages/loki/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/loki/trunk/debian/README.Debian 2008-02-26 20:17:22 UTC (rev 1477)
@@ -0,0 +1,15 @@
+loki for Debian
+---------------
+
+Notice that the Perl scripts ("utils") provided with Loki have been renamed
+as follows:
+
+ count.pl -> loki_count
+ dist.pl -> loki_dist
+ freq.pl -> loki_freq
+ loki_ext.pl -> loki_ext
+ sort_error.pl -> loki_sort_error
+
+so please be aware when reading the documentation and using these programs.
+
+ -- Carleos Artime <carleos at pinon.ccu.uniovi.es>, Thu, 31 Oct 2002 17:22:58 +0100
Added: trunk/packages/loki/trunk/debian/changelog
===================================================================
--- trunk/packages/loki/trunk/debian/changelog (rev 0)
+++ trunk/packages/loki/trunk/debian/changelog 2008-02-26 20:17:22 UTC (rev 1477)
@@ -0,0 +1,36 @@
+loki (2.4.6-1) unstable; urgency=low
+
+ * First official release
+ closes: #155071
+ * New upstream release.
+ * Changed section in debian/control from "misc" to "science".
+ * Added homepage to package description in debian/control.
+ * Split up into two packages (loki, loki-doc).
+ * Changes by Andreas Tille <tille at debian.org>
+ - Added "Suggests: loki-doc" to loki
+ - Changed "Depends" to "Suggests: loki" in loki-doc to enable
+ reading online documentation without installing the binary package
+ - used debian/loki-doc.docs and dh_installdocs to install documentation
+ - moved debian/lokifaq.doc-base to debian/loki-doc.doc-base.lokifaq and
+ debian/lokimanual.doc-base debian/loki-doc.doc-base.lokimanual
+ - Added debian/loci-doc.README.Debian to give a hint at the LaTeX
+ source of the documentation.
+
+ -- Carleos Artime <carleos at pinon.ccu.uniovi.es> Fri, 25 Apr 2003 18:56:57 +0200
+
+loki (2.4.5-1) unstable; urgency=low
+
+ * Initial Release.
+ * Having read "man dh_installdocs", split "debian/doc-base" in two files.
+ * Included a "menu" entry that simply shows loki's man page.
+ * Renamed utils/loki_ext.in to utils/ext.in.
+ * Modified utils/Makefile.in to rename executables: count.pl, dist.pl,
+ freq.pl, loki_ext.pl, sort_error.pl, are now loki_count, loki_dist,
+ loki_freq, loki_ext, and loki_sort_error.
+ * Fixed copyright-lists-upstream-authors-with-dh_make-boilerplate bug
+ by just removing (s) behind Author
+ * Appended upstream COPYRIGHT to debian/copyright to get it included
+ into the Debian package
+ * Standards-Version: 3.5.9
+
+ -- Carleos Artime <carleos at pinon.ccu.uniovi.es> Sat, 5 Apr 2003 18:56:57 +0200
Added: trunk/packages/loki/trunk/debian/check_het.1
===================================================================
--- trunk/packages/loki/trunk/debian/check_het.1 (rev 0)
+++ trunk/packages/loki/trunk/debian/check_het.1 2008-02-26 20:17:22 UTC (rev 1477)
@@ -0,0 +1,58 @@
+.\" Hey, EMACS: -*- nroff -*-
+.\" First parameter, NAME, should be all caps
+.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
+.\" other parameters are allowed: see man(7), man(1)
+.TH LOKI 1 "october 31, 2002"
+.\" Please adjust this date whenever revising the manpage.
+.\"
+.\" Some roff macros, for reference:
+.\" .nh disable hyphenation
+.\" .hy enable hyphenation
+.\" .ad l left justify
+.\" .ad b justify to both left and right margins
+.\" .nf disable filling
+.\" .fi enable filling
+.\" .br insert line break
+.\" .sp <n> insert n+1 empty lines
+.\" for manpage-specific macros, see man(7)
+.SH NAME
+loki \- Reversible jump MCMC linkage analysis in general pedigrees
+.SH SYNOPSIS
+.B prep
+.RI controlfile
+.br
+.B loki
+.RI -v
+.br
+.B loki
+.RI paramfile
+.SH DESCRIPTION
+This manual page documents briefly the
+.B prep
+and
+.B loki
+commands. Other post-hoc analysis scripts are available; please see
+the complete documentation.
+This manual page was written for the Debian GNU/Linux distribution
+because the original program does not have a manual page.
+Instead, it has documentation in PostScript format; see below.
+.PP
+.\" TeX users may be more comfortable with the \fB<whatever>\fP and
+.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
+.\" respectively.
+\fBloki\fP, written by Simon C. Heath, implements segregation and linkage
+analysis on possibly large and complex pedigrees, by means of a Reversible
+Jump Markov Chain Monte Carlo technique.
+\fBprep\fP performs previous data preparation.
+.SH OPTIONS
+.TP
+.B \-v
+Show version of the program.
+.SH SEE ALSO
+The programs are documented fully in
+.IR /usr/share/doc/loki/,
+available on-line at
+.IR http://loki.homeunix.net/ .
+.SH AUTHOR
+This manual page was written by Carleos Artime <carleos at pinon.ccu.uniovi.es>,
+for the Debian GNU/Linux system (but may be used by others).
Added: trunk/packages/loki/trunk/debian/compat
===================================================================
--- trunk/packages/loki/trunk/debian/compat (rev 0)
+++ trunk/packages/loki/trunk/debian/compat 2008-02-26 20:17:22 UTC (rev 1477)
@@ -0,0 +1 @@
+4
Added: trunk/packages/loki/trunk/debian/control
===================================================================
--- trunk/packages/loki/trunk/debian/control (rev 0)
+++ trunk/packages/loki/trunk/debian/control 2008-02-26 20:17:22 UTC (rev 1477)
@@ -0,0 +1,29 @@
+Source: loki
+Section: science
+Priority: optional
+Maintainer: Carleos Artime <carleos at pinon.ccu.uniovi.es>
+Build-Depends: debhelper (>> 4.0.0)
+Standards-Version: 3.5.9
+XBCS-URL: http://loki.homeunix.net.
+
+Package: loki
+Architecture: any
+Depends: ${shlibs:Depends}
+Suggests: loki-doc
+Description: [Biology] MCMC linkage analysis on general pedigrees
+ Performs Markov chain Monte Carlo multipoint linkage analysis on large,
+ complex pedigrees. The current package supports analyses on quantitative
+ traits only, although this restriction will be lifted in later versions.
+ Joint estimation of QTL number, position and effects uses Reversible Jump
+ MCMC. It is also possible to perform affected only IBD sharing analyses.
+ .
+ Homepage: http://loki.homeunix.net.
+
+Package: loki-doc
+Architecture: all
+Suggests: loki
+Description: [Biology] Postscript manual for loki
+ Documentation on how to use Simon Heath's "prep" and "loki" tools
+ for MCMC genetic linkage and IBD analysis on general pedigrees.
+ .
+ Homepage: http://loki.homeunix.net.
\ No newline at end of file
Added: trunk/packages/loki/trunk/debian/copyright
===================================================================
--- trunk/packages/loki/trunk/debian/copyright (rev 0)
+++ trunk/packages/loki/trunk/debian/copyright 2008-02-26 20:17:22 UTC (rev 1477)
@@ -0,0 +1,35 @@
+This package was debianized by Carleos Artime <carleos at pinon.ccu.uniovi.es> on
+Thu, 31 Oct 2002 17:22:58 +0100.
+
+It was downloaded from http://loki.homeunix.net.
+
+Upstream Author: Simon C. Heath <heath at cng.fr>
+
+Copyright:
+
+(c) 1997-2002 by Simon C. Heath.
+
+Loki source is available under a modified version of the BSD license:
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions
+are met:
+
+Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+Redistributions in binary form must reproduce the above copyright
+notice, this list of conditions and the following disclaimer in the
+documentation and/or other materials provided with the distribution.
+The name of the author may not be used to endorse or promote products
+derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``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 AUTHOR 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.
Added: trunk/packages/loki/trunk/debian/hist.1
===================================================================
--- trunk/packages/loki/trunk/debian/hist.1 (rev 0)
+++ trunk/packages/loki/trunk/debian/hist.1 2008-02-26 20:17:22 UTC (rev 1477)
@@ -0,0 +1,58 @@
+.\" Hey, EMACS: -*- nroff -*-
+.\" First parameter, NAME, should be all caps
+.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
+.\" other parameters are allowed: see man(7), man(1)
+.TH LOKI 1 "october 31, 2002"
+.\" Please adjust this date whenever revising the manpage.
+.\"
+.\" Some roff macros, for reference:
+.\" .nh disable hyphenation
+.\" .hy enable hyphenation
+.\" .ad l left justify
+.\" .ad b justify to both left and right margins
+.\" .nf disable filling
+.\" .fi enable filling
+.\" .br insert line break
+.\" .sp <n> insert n+1 empty lines
+.\" for manpage-specific macros, see man(7)
+.SH NAME
+loki \- Reversible jump MCMC linkage analysis in general pedigrees
+.SH SYNOPSIS
+.B prep
+.RI controlfile
+.br
+.B loki
+.RI -v
+.br
+.B loki
+.RI paramfile
+.SH DESCRIPTION
+This manual page documents briefly the
+.B prep
+and
+.B loki
+commands. Other post-hoc analysis scripts are available; please see
+the complete documentation.
+This manual page was written for the Debian GNU/Linux distribution
+because the original program does not have a manual page.
+Instead, it has documentation in PostScript format; see below.
+.PP
+.\" TeX users may be more comfortable with the \fB<whatever>\fP and
+.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
+.\" respectively.
+\fBloki\fP, written by Simon C. Heath, implements segregation and linkage
+analysis on possibly large and complex pedigrees, by means of a Reversible
+Jump Markov Chain Monte Carlo technique.
+\fBprep\fP performs previous data preparation.
+.SH OPTIONS
+.TP
+.B \-v
+Show version of the program.
+.SH SEE ALSO
+The programs are documented fully in
+.IR /usr/share/doc/loki/,
+available on-line at
+.IR http://loki.homeunix.net/ .
+.SH AUTHOR
+This manual page was written by Carleos Artime <carleos at pinon.ccu.uniovi.es>,
+for the Debian GNU/Linux system (but may be used by others).
Added: trunk/packages/loki/trunk/debian/loki-doc.README.Debian
===================================================================
--- trunk/packages/loki/trunk/debian/loki-doc.README.Debian (rev 0)
+++ trunk/packages/loki/trunk/debian/loki-doc.README.Debian 2008-02-26 20:17:22 UTC (rev 1477)
@@ -0,0 +1,3 @@
+This is the documentation for the loki package. The source package
+of loki also contains the LaTeX source of these PostScript files.
+
Added: trunk/packages/loki/trunk/debian/loki-doc.doc-base.lokifaq
===================================================================
--- trunk/packages/loki/trunk/debian/loki-doc.doc-base.lokifaq (rev 0)
+++ trunk/packages/loki/trunk/debian/loki-doc.doc-base.lokifaq 2008-02-26 20:17:22 UTC (rev 1477)
@@ -0,0 +1,10 @@
+Document: lokifaq
+Title: Loki Manual
+Author: Simon C. Heath
+Abstract: This document answers frequently
+ asked questions about Loki.
+Section: Apps/Science
+
+Format: postscript
+Files: /usr/share/doc/loki/docs/loki_faq.ps.gz
+
Added: trunk/packages/loki/trunk/debian/loki-doc.doc-base.lokimanual
===================================================================
--- trunk/packages/loki/trunk/debian/loki-doc.doc-base.lokimanual (rev 0)
+++ trunk/packages/loki/trunk/debian/loki-doc.doc-base.lokimanual 2008-02-26 20:17:22 UTC (rev 1477)
@@ -0,0 +1,11 @@
+Document: lokimanual
+Title: Loki Manual
+Author: Simon C. Heath
+Abstract: This manual describes what loki is
+ and how it can be used to perform genetic
+ linkage analyses.
+Section: Apps/Science
+
+Format: postscript
+Files: /usr/share/doc/loki/docs/loki_doc.ps.gz
+
Added: trunk/packages/loki/trunk/debian/loki-doc.docs
===================================================================
--- trunk/packages/loki/trunk/debian/loki-doc.docs (rev 0)
+++ trunk/packages/loki/trunk/debian/loki-doc.docs 2008-02-26 20:17:22 UTC (rev 1477)
@@ -0,0 +1 @@
+docs/*.ps
Added: trunk/packages/loki/trunk/debian/loki.1
===================================================================
--- trunk/packages/loki/trunk/debian/loki.1 (rev 0)
+++ trunk/packages/loki/trunk/debian/loki.1 2008-02-26 20:17:22 UTC (rev 1477)
@@ -0,0 +1,58 @@
+.\" Hey, EMACS: -*- nroff -*-
+.\" First parameter, NAME, should be all caps
+.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
+.\" other parameters are allowed: see man(7), man(1)
+.TH LOKI 1 "october 31, 2002"
+.\" Please adjust this date whenever revising the manpage.
+.\"
+.\" Some roff macros, for reference:
+.\" .nh disable hyphenation
+.\" .hy enable hyphenation
+.\" .ad l left justify
+.\" .ad b justify to both left and right margins
+.\" .nf disable filling
+.\" .fi enable filling
+.\" .br insert line break
+.\" .sp <n> insert n+1 empty lines
+.\" for manpage-specific macros, see man(7)
+.SH NAME
+loki \- Reversible jump MCMC linkage analysis in general pedigrees
+.SH SYNOPSIS
+.B prep
+.RI controlfile
+.br
+.B loki
+.RI -v
+.br
+.B loki
+.RI paramfile
+.SH DESCRIPTION
+This manual page documents briefly the
+.B prep
+and
+.B loki
+commands. Other post-hoc analysis scripts are available; please see
+the complete documentation.
+This manual page was written for the Debian GNU/Linux distribution
+because the original program does not have a manual page.
+Instead, it has documentation in PostScript format; see below.
+.PP
+.\" TeX users may be more comfortable with the \fB<whatever>\fP and
+.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
+.\" respectively.
+\fBloki\fP, written by Simon C. Heath, implements segregation and linkage
+analysis on possibly large and complex pedigrees, by means of a Reversible
+Jump Markov Chain Monte Carlo technique.
+\fBprep\fP performs previous data preparation.
+.SH OPTIONS
+.TP
+.B \-v
+Show version of the program.
+.SH SEE ALSO
+The programs are documented fully in
+.IR /usr/share/doc/loki/,
+available on-line at
+.IR http://loki.homeunix.net/.
+.SH AUTHOR
+This manual page was written by Carleos Artime <carleos at pinon.ccu.uniovi.es>,
+for the Debian GNU/Linux system (but may be used by others).
Added: trunk/packages/loki/trunk/debian/loki.dirs
===================================================================
--- trunk/packages/loki/trunk/debian/loki.dirs (rev 0)
+++ trunk/packages/loki/trunk/debian/loki.dirs 2008-02-26 20:17:22 UTC (rev 1477)
@@ -0,0 +1,3 @@
+usr/bin
+usr/share/doc/loki
+usr/share/man/man1
Added: trunk/packages/loki/trunk/debian/loki.docs
===================================================================
--- trunk/packages/loki/trunk/debian/loki.docs (rev 0)
+++ trunk/packages/loki/trunk/debian/loki.docs 2008-02-26 20:17:22 UTC (rev 1477)
@@ -0,0 +1,4 @@
+README
+README.known_systems
+README.multiple_records
+README.parallel_runs
Added: trunk/packages/loki/trunk/debian/loki_count.1
===================================================================
--- trunk/packages/loki/trunk/debian/loki_count.1 (rev 0)
+++ trunk/packages/loki/trunk/debian/loki_count.1 2008-02-26 20:17:22 UTC (rev 1477)
@@ -0,0 +1,58 @@
+.\" Hey, EMACS: -*- nroff -*-
+.\" First parameter, NAME, should be all caps
+.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
+.\" other parameters are allowed: see man(7), man(1)
+.TH LOKI 1 "october 31, 2002"
+.\" Please adjust this date whenever revising the manpage.
+.\"
+.\" Some roff macros, for reference:
+.\" .nh disable hyphenation
+.\" .hy enable hyphenation
+.\" .ad l left justify
+.\" .ad b justify to both left and right margins
+.\" .nf disable filling
+.\" .fi enable filling
+.\" .br insert line break
+.\" .sp <n> insert n+1 empty lines
+.\" for manpage-specific macros, see man(7)
+.SH NAME
+loki \- Reversible jump MCMC linkage analysis in general pedigrees
+.SH SYNOPSIS
+.B prep
+.RI controlfile
+.br
+.B loki
+.RI -v
+.br
+.B loki
+.RI paramfile
+.SH DESCRIPTION
+This manual page documents briefly the
+.B prep
+and
+.B loki
+commands. Other post-hoc analysis scripts are available; please see
+the complete documentation.
+This manual page was written for the Debian GNU/Linux distribution
+because the original program does not have a manual page.
+Instead, it has documentation in PostScript format; see below.
+.PP
+.\" TeX users may be more comfortable with the \fB<whatever>\fP and
+.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
+.\" respectively.
+\fBloki\fP, written by Simon C. Heath, implements segregation and linkage
+analysis on possibly large and complex pedigrees, by means of a Reversible
+Jump Markov Chain Monte Carlo technique.
+\fBprep\fP performs previous data preparation.
+.SH OPTIONS
+.TP
+.B \-v
+Show version of the program.
+.SH SEE ALSO
+The programs are documented fully in
+.IR /usr/share/doc/loki/,
+available on-line at
+.IR http://loki.homeunix.net/ .
+.SH AUTHOR
+This manual page was written by Carleos Artime <carleos at pinon.ccu.uniovi.es>,
+for the Debian GNU/Linux system (but may be used by others).
Added: trunk/packages/loki/trunk/debian/loki_dist.1
===================================================================
--- trunk/packages/loki/trunk/debian/loki_dist.1 (rev 0)
+++ trunk/packages/loki/trunk/debian/loki_dist.1 2008-02-26 20:17:22 UTC (rev 1477)
@@ -0,0 +1,58 @@
+.\" Hey, EMACS: -*- nroff -*-
+.\" First parameter, NAME, should be all caps
+.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
+.\" other parameters are allowed: see man(7), man(1)
+.TH LOKI 1 "october 31, 2002"
+.\" Please adjust this date whenever revising the manpage.
+.\"
+.\" Some roff macros, for reference:
+.\" .nh disable hyphenation
+.\" .hy enable hyphenation
+.\" .ad l left justify
+.\" .ad b justify to both left and right margins
+.\" .nf disable filling
+.\" .fi enable filling
+.\" .br insert line break
+.\" .sp <n> insert n+1 empty lines
+.\" for manpage-specific macros, see man(7)
+.SH NAME
+loki \- Reversible jump MCMC linkage analysis in general pedigrees
+.SH SYNOPSIS
+.B prep
+.RI controlfile
+.br
+.B loki
+.RI -v
+.br
+.B loki
+.RI paramfile
+.SH DESCRIPTION
+This manual page documents briefly the
+.B prep
+and
+.B loki
+commands. Other post-hoc analysis scripts are available; please see
+the complete documentation.
+This manual page was written for the Debian GNU/Linux distribution
+because the original program does not have a manual page.
+Instead, it has documentation in PostScript format; see below.
+.PP
+.\" TeX users may be more comfortable with the \fB<whatever>\fP and
+.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
+.\" respectively.
+\fBloki\fP, written by Simon C. Heath, implements segregation and linkage
+analysis on possibly large and complex pedigrees, by means of a Reversible
+Jump Markov Chain Monte Carlo technique.
+\fBprep\fP performs previous data preparation.
+.SH OPTIONS
+.TP
+.B \-v
+Show version of the program.
+.SH SEE ALSO
+The programs are documented fully in
+.IR /usr/share/doc/loki/,
+available on-line at
+.IR http://loki.homeunix.net/ .
+.SH AUTHOR
+This manual page was written by Carleos Artime <carleos at pinon.ccu.uniovi.es>,
+for the Debian GNU/Linux system (but may be used by others).
Added: trunk/packages/loki/trunk/debian/loki_ext.1
===================================================================
--- trunk/packages/loki/trunk/debian/loki_ext.1 (rev 0)
+++ trunk/packages/loki/trunk/debian/loki_ext.1 2008-02-26 20:17:22 UTC (rev 1477)
@@ -0,0 +1,58 @@
+.\" Hey, EMACS: -*- nroff -*-
+.\" First parameter, NAME, should be all caps
+.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
+.\" other parameters are allowed: see man(7), man(1)
+.TH LOKI 1 "october 31, 2002"
+.\" Please adjust this date whenever revising the manpage.
+.\"
+.\" Some roff macros, for reference:
+.\" .nh disable hyphenation
+.\" .hy enable hyphenation
+.\" .ad l left justify
+.\" .ad b justify to both left and right margins
+.\" .nf disable filling
+.\" .fi enable filling
+.\" .br insert line break
+.\" .sp <n> insert n+1 empty lines
+.\" for manpage-specific macros, see man(7)
+.SH NAME
+loki \- Reversible jump MCMC linkage analysis in general pedigrees
+.SH SYNOPSIS
+.B prep
+.RI controlfile
+.br
+.B loki
+.RI -v
+.br
+.B loki
+.RI paramfile
+.SH DESCRIPTION
+This manual page documents briefly the
+.B prep
+and
+.B loki
+commands. Other post-hoc analysis scripts are available; please see
+the complete documentation.
+This manual page was written for the Debian GNU/Linux distribution
+because the original program does not have a manual page.
+Instead, it has documentation in PostScript format; see below.
+.PP
+.\" TeX users may be more comfortable with the \fB<whatever>\fP and
+.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
+.\" respectively.
+\fBloki\fP, written by Simon C. Heath, implements segregation and linkage
+analysis on possibly large and complex pedigrees, by means of a Reversible
+Jump Markov Chain Monte Carlo technique.
+\fBprep\fP performs previous data preparation.
+.SH OPTIONS
+.TP
+.B \-v
+Show version of the program.
+.SH SEE ALSO
+The programs are documented fully in
+.IR /usr/share/doc/loki/,
+available on-line at
+.IR http://loki.homeunix.net/ .
+.SH AUTHOR
+This manual page was written by Carleos Artime <carleos at pinon.ccu.uniovi.es>,
+for the Debian GNU/Linux system (but may be used by others).
Added: trunk/packages/loki/trunk/debian/loki_freq.1
===================================================================
--- trunk/packages/loki/trunk/debian/loki_freq.1 (rev 0)
+++ trunk/packages/loki/trunk/debian/loki_freq.1 2008-02-26 20:17:22 UTC (rev 1477)
@@ -0,0 +1,58 @@
+.\" Hey, EMACS: -*- nroff -*-
+.\" First parameter, NAME, should be all caps
+.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
+.\" other parameters are allowed: see man(7), man(1)
+.TH LOKI 1 "october 31, 2002"
+.\" Please adjust this date whenever revising the manpage.
+.\"
+.\" Some roff macros, for reference:
+.\" .nh disable hyphenation
+.\" .hy enable hyphenation
+.\" .ad l left justify
+.\" .ad b justify to both left and right margins
+.\" .nf disable filling
+.\" .fi enable filling
+.\" .br insert line break
+.\" .sp <n> insert n+1 empty lines
+.\" for manpage-specific macros, see man(7)
+.SH NAME
+loki \- Reversible jump MCMC linkage analysis in general pedigrees
+.SH SYNOPSIS
+.B prep
+.RI controlfile
+.br
+.B loki
+.RI -v
+.br
+.B loki
+.RI paramfile
+.SH DESCRIPTION
+This manual page documents briefly the
+.B prep
+and
+.B loki
+commands. Other post-hoc analysis scripts are available; please see
+the complete documentation.
+This manual page was written for the Debian GNU/Linux distribution
+because the original program does not have a manual page.
+Instead, it has documentation in PostScript format; see below.
+.PP
+.\" TeX users may be more comfortable with the \fB<whatever>\fP and
+.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
+.\" respectively.
+\fBloki\fP, written by Simon C. Heath, implements segregation and linkage
+analysis on possibly large and complex pedigrees, by means of a Reversible
+Jump Markov Chain Monte Carlo technique.
+\fBprep\fP performs previous data preparation.
+.SH OPTIONS
+.TP
+.B \-v
+Show version of the program.
+.SH SEE ALSO
+The programs are documented fully in
+.IR /usr/share/doc/loki/,
+available on-line at
+.IR http://loki.homeunix.net/ .
+.SH AUTHOR
+This manual page was written by Carleos Artime <carleos at pinon.ccu.uniovi.es>,
+for the Debian GNU/Linux system (but may be used by others).
Added: trunk/packages/loki/trunk/debian/loki_sort_error.1
===================================================================
--- trunk/packages/loki/trunk/debian/loki_sort_error.1 (rev 0)
+++ trunk/packages/loki/trunk/debian/loki_sort_error.1 2008-02-26 20:17:22 UTC (rev 1477)
@@ -0,0 +1,58 @@
+.\" Hey, EMACS: -*- nroff -*-
+.\" First parameter, NAME, should be all caps
+.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
+.\" other parameters are allowed: see man(7), man(1)
+.TH LOKI 1 "october 31, 2002"
+.\" Please adjust this date whenever revising the manpage.
+.\"
+.\" Some roff macros, for reference:
+.\" .nh disable hyphenation
+.\" .hy enable hyphenation
+.\" .ad l left justify
+.\" .ad b justify to both left and right margins
+.\" .nf disable filling
+.\" .fi enable filling
+.\" .br insert line break
+.\" .sp <n> insert n+1 empty lines
+.\" for manpage-specific macros, see man(7)
+.SH NAME
+loki \- Reversible jump MCMC linkage analysis in general pedigrees
+.SH SYNOPSIS
+.B prep
+.RI controlfile
+.br
+.B loki
+.RI -v
+.br
+.B loki
+.RI paramfile
+.SH DESCRIPTION
+This manual page documents briefly the
+.B prep
+and
+.B loki
+commands. Other post-hoc analysis scripts are available; please see
+the complete documentation.
+This manual page was written for the Debian GNU/Linux distribution
+because the original program does not have a manual page.
+Instead, it has documentation in PostScript format; see below.
+.PP
+.\" TeX users may be more comfortable with the \fB<whatever>\fP and
+.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
+.\" respectively.
+\fBloki\fP, written by Simon C. Heath, implements segregation and linkage
+analysis on possibly large and complex pedigrees, by means of a Reversible
+Jump Markov Chain Monte Carlo technique.
+\fBprep\fP performs previous data preparation.
+.SH OPTIONS
+.TP
+.B \-v
+Show version of the program.
+.SH SEE ALSO
+The programs are documented fully in
+.IR /usr/share/doc/loki/,
+available on-line at
+.IR http://loki.homeunix.net/ .
+.SH AUTHOR
+This manual page was written by Carleos Artime <carleos at pinon.ccu.uniovi.es>,
+for the Debian GNU/Linux system (but may be used by others).
Added: trunk/packages/loki/trunk/debian/menu
===================================================================
--- trunk/packages/loki/trunk/debian/menu (rev 0)
+++ trunk/packages/loki/trunk/debian/menu 2008-02-26 20:17:22 UTC (rev 1477)
@@ -0,0 +1,2 @@
+?package(loki):needs=text section=Apps/Science\
+ title="loki" command="man loki"
Added: trunk/packages/loki/trunk/debian/prep.1
===================================================================
--- trunk/packages/loki/trunk/debian/prep.1 (rev 0)
+++ trunk/packages/loki/trunk/debian/prep.1 2008-02-26 20:17:22 UTC (rev 1477)
@@ -0,0 +1,58 @@
+.\" Hey, EMACS: -*- nroff -*-
+.\" First parameter, NAME, should be all caps
+.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
+.\" other parameters are allowed: see man(7), man(1)
+.TH LOKI 1 "october 31, 2002"
+.\" Please adjust this date whenever revising the manpage.
+.\"
+.\" Some roff macros, for reference:
+.\" .nh disable hyphenation
+.\" .hy enable hyphenation
+.\" .ad l left justify
+.\" .ad b justify to both left and right margins
+.\" .nf disable filling
+.\" .fi enable filling
+.\" .br insert line break
+.\" .sp <n> insert n+1 empty lines
+.\" for manpage-specific macros, see man(7)
+.SH NAME
+loki \- Reversible jump MCMC linkage analysis in general pedigrees
+.SH SYNOPSIS
+.B prep
+.RI controlfile
+.br
+.B loki
+.RI -v
+.br
+.B loki
+.RI paramfile
+.SH DESCRIPTION
+This manual page documents briefly the
+.B prep
+and
+.B loki
+commands. Other post-hoc analysis scripts are available; please see
+the complete documentation.
+This manual page was written for the Debian GNU/Linux distribution
+because the original program does not have a manual page.
+Instead, it has documentation in PostScript format; see below.
+.PP
+.\" TeX users may be more comfortable with the \fB<whatever>\fP and
+.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
+.\" respectively.
+\fBloki\fP, written by Simon C. Heath, implements segregation and linkage
+analysis on possibly large and complex pedigrees, by means of a Reversible
+Jump Markov Chain Monte Carlo technique.
+\fBprep\fP performs previous data preparation.
+.SH OPTIONS
+.TP
+.B \-v
+Show version of the program.
+.SH SEE ALSO
+The programs are documented fully in
+.IR /usr/share/doc/loki/,
+available on-line at
+.IR http://loki.homeunix.net/ .
+.SH AUTHOR
+This manual page was written by Carleos Artime <carleos at pinon.ccu.uniovi.es>,
+for the Debian GNU/Linux system (but may be used by others).
Added: trunk/packages/loki/trunk/debian/qavg.1
===================================================================
--- trunk/packages/loki/trunk/debian/qavg.1 (rev 0)
+++ trunk/packages/loki/trunk/debian/qavg.1 2008-02-26 20:17:22 UTC (rev 1477)
@@ -0,0 +1,58 @@
+.\" Hey, EMACS: -*- nroff -*-
+.\" First parameter, NAME, should be all caps
+.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
+.\" other parameters are allowed: see man(7), man(1)
+.TH LOKI 1 "october 31, 2002"
+.\" Please adjust this date whenever revising the manpage.
+.\"
+.\" Some roff macros, for reference:
+.\" .nh disable hyphenation
+.\" .hy enable hyphenation
+.\" .ad l left justify
+.\" .ad b justify to both left and right margins
+.\" .nf disable filling
+.\" .fi enable filling
+.\" .br insert line break
+.\" .sp <n> insert n+1 empty lines
+.\" for manpage-specific macros, see man(7)
+.SH NAME
+loki \- Reversible jump MCMC linkage analysis in general pedigrees
+.SH SYNOPSIS
+.B prep
+.RI controlfile
+.br
+.B loki
+.RI -v
+.br
+.B loki
+.RI paramfile
+.SH DESCRIPTION
+This manual page documents briefly the
+.B prep
+and
+.B loki
+commands. Other post-hoc analysis scripts are available; please see
+the complete documentation.
+This manual page was written for the Debian GNU/Linux distribution
+because the original program does not have a manual page.
+Instead, it has documentation in PostScript format; see below.
+.PP
+.\" TeX users may be more comfortable with the \fB<whatever>\fP and
+.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
+.\" respectively.
+\fBloki\fP, written by Simon C. Heath, implements segregation and linkage
+analysis on possibly large and complex pedigrees, by means of a Reversible
+Jump Markov Chain Monte Carlo technique.
+\fBprep\fP performs previous data preparation.
+.SH OPTIONS
+.TP
+.B \-v
+Show version of the program.
+.SH SEE ALSO
+The programs are documented fully in
+.IR /usr/share/doc/loki/,
+available on-line at
+.IR http://loki.homeunix.net/ .
+.SH AUTHOR
+This manual page was written by Carleos Artime <carleos at pinon.ccu.uniovi.es>,
+for the Debian GNU/Linux system (but may be used by others).
Added: trunk/packages/loki/trunk/debian/rules
===================================================================
--- trunk/packages/loki/trunk/debian/rules (rev 0)
+++ trunk/packages/loki/trunk/debian/rules 2008-02-26 20:17:22 UTC (rev 1477)
@@ -0,0 +1,115 @@
+#!/usr/bin/make -f
+# debian/rules for loki
+# Carleos Artime (carleos at pinon.ccu.uniovi.es)
+# GPL
+
+# added after Andreas Tille's Makefile for fastlink:
+pkg=loki
+doc=$(pkg)-doc
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+# These are used for cross-compiling and for saving the configure script
+# from having to guess our platform (since we know it already)
+DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE)
+DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
+
+
+ifneq (,$(findstring debug,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -g
+endif
+ifeq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS)))
+ INSTALL_PROGRAM += -s
+endif
+
+config.status: configure
+ dh_testdir
+ # Add here commands to configure the package.
+ ./configure --host=$(DEB_HOST_GNU_TYPE) --build=$(DEB_BUILD_GNU_TYPE) --prefix=/usr --mandir=\$${prefix}/share/man --infodir=\$${prefix}/share/info
+
+
+build: build-stamp
+
+build-stamp: config.status
+ dh_testdir
+
+ # Add here commands to compile the package.
+ $(MAKE)
+ #/usr/bin/docbook-to-man debian/loki.sgml > loki.1
+
+ touch build-stamp
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp
+
+ # Add here commands to clean up after the build process.
+ -$(MAKE) distclean
+ -test -r /usr/share/misc/config.sub && \
+ cp -f /usr/share/misc/config.sub config.sub
+ -test -r /usr/share/misc/config.guess && \
+ cp -f /usr/share/misc/config.guess config.guess
+
+
+ dh_clean
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+
+ # Add here commands to install the package into debian/loki.
+ $(MAKE) install prefix=$(CURDIR)/debian/loki/usr
+
+ # Added after fastlink's makefile to split up into two packages:
+# mkdir -p `pwd`/debian/$(doc)/usr/share/doc/$(pkg)/docs
+# cp -a `pwd`/docs/*.ps `pwd`/debian/$(doc)/usr/share/doc/$(pkg)/docs
+# ln -s $(pkg) `pwd`/debian/$(doc)/usr/share/doc/$(doc)
+
+# Build architecture-independent files here.
+binary-indep: build install
+ dh_testdir -i
+ dh_testroot -i
+# dh_installdebconf
+ dh_installdocs -i
+ dh_installchangelogs -i
+ dh_link -i
+# dh_strip
+ dh_compress -i
+ dh_fixperms -i
+# dh_makeshlibs
+ dh_installdeb -i
+# dh_perl
+# dh_shlibdeps
+ dh_gencontrol -i
+ dh_md5sums -i
+ dh_builddeb -i
+
+
+# Build architecture-dependent files here.
+binary-arch: build install
+ dh_testdir -a
+ dh_testroot -a
+# dh_installdebconf
+ dh_installdocs -a
+# dh_installexamples
+ dh_installmenu -a
+ dh_installman -a debian/*.1
+ dh_installchangelogs -a Changes
+ dh_link -a
+ dh_strip -a
+ dh_compress -a
+ dh_fixperms -a
+# dh_makeshlibs
+ dh_installdeb -a
+# dh_perl
+ dh_shlibdeps -a
+ dh_gencontrol -a
+ dh_md5sums -a
+ dh_builddeb -a
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install
Property changes on: trunk/packages/loki/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/loki/trunk/debian/watch
===================================================================
--- trunk/packages/loki/trunk/debian/watch (rev 0)
+++ trunk/packages/loki/trunk/debian/watch 2008-02-26 20:17:22 UTC (rev 1477)
@@ -0,0 +1,6 @@
+# Example watch control file for uscan
+# Rename this file to "watch" and then you can run the "uscan" command
+# to check for upstream updates and more.
+# Site Directory Pattern Version Script
+version=2
+http://loki.homeunix.net/tar/loki_(.*)\.tar\.gz debian uupdate
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