Commit 1468a53a authored by Andreas Tille's avatar Andreas Tille

New upstream version 2.4.7.4

parent 3b527d8d
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Redistributions of source code must retain the above copyright
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SHELL = /bin/sh
SUBDIRS = libsrc prepsrc lokisrc utils
INSTALLDIRS = prepsrc lokisrc utils
SED = @SED@
PERL = @PERL@
@SET_MAKE@
all: progs
progs: include/config.h depend
for subdir in $(SUBDIRS); do \
(cd $$subdir; $(MAKE)) \
done
tests:
(cd test; $(MAKE))
install: progs
for subdir in $(INSTALLDIRS); do \
(cd $$subdir; $(MAKE) install) \
done
depend: include/config.h
for subdir in $(SUBDIRS); do \
(cd $$subdir; $(MAKE) depend) \
done
touch depend
clean:
for subdir in $(SUBDIRS) test; do \
(cd $$subdir; $(MAKE) clean) \
done
rm -f *~ core a.out *.bak depend
distclean:
rm -f *~ core a.out *.bak include/config.h config.status \
config.log config.cache loki_cnt depend
for subdir in $(SUBDIRS) test; do \
(cd $$subdir; $(MAKE) distclean) \
done
rm -f Makefile
Loki 2.4.6 - Simon Heath - April 2003
This package contains the source and examples for Loki version 2.3. Loki
performs Markov chain Monte Carlo (MCMC) multivariate linkage analysis on
general pedigrees. The current package supports analyses on quantitative
traits only, although this restriction will be lifted in later versions. For
more details see the files in the docs/ subdirectory. Changes from previous
versions are (sometimes) listed in the Changes file in this directory.
** Making **
Making the package should hopefully just involve typing:
./configure
make
Choices for the C compiler and options can be fixed by setting the shell
environment variables CC and CFLAGS before running ./configure i.e.,
CC=gcc CFLAGS='-O2 -pedantic -Wall -W' ./configure
make
** Testing **
The package has been mostly tested with gcc and GNU make, though it should
work with alternative compilers and make utilities with little or no
modification. If you have problems compiling please retry with the GNU
tools. Whether or not this works, please send me an emai at
heath@hardy.mskcc.org to let me know the machine, operating system, compiler
and make utility used, and what error messages were produced.
To run the programs against test datasets with known results, type make
tests. If you get an output like:
JV test 1
JV test 2
GAW9 test
JV restart test
and no errors reported, then everything was successful. If not, then type:
make clean
make 2>&1 >error.log
and email the file error.log to me at heath@hardy.mskcc.org, with a
description of the machine you are using (type uname -a), the compiler and
which compiler flags were used.
** Installing **
Installing the package can be done by typing make install. By default, the
programs and scripts are installed to the bin sub-directory of the main loki
directory. This behaviour can be changed by giving the --prefix
option to configure. For example, to install to /usr/local/bin type:
./configure --prefix=/usr/local
loki_2.3 has been compiled and tested on the following systems:
Solaris sparc 5.8/5.7 (gcc)
Solaris intel 5.8 (gcc)
FreeBSD intel 4.0-4.5 (gcc)
OpenBSD intel 2.7-3.1 (gcc)
OSF1 V4.0 alpha (gcc,cc)
Linux intel 2.2,2.4 (gcc)
Linux sparc 2.2,2.4 (gcc)
Linux alpha 2.2,2.4 (gcc,ccc [dec compiler])
Irix R10000 6.5 (cc - 32 bit)
Irix R10000 6.5 (cc - 64 bit)
MacOSX G4 10.04,10.1 (gcc)
AIX 4.3.3 (gcc)
Information on successes/failures on other systems gratefully received.
Multiple records in Loki - change in default behaviour
The default for all variables is now CONSTANT. This means that if multiple
records (lines) are read in for an individual, checks will be made that they
match, and all variables will be assumed to form 1 logical record.
If true multiple records are present (i.e., an individual was measured
multiple times), then sets of variables can be switched using the (new)
MULTIPLE command. To revert back to the previous behaviour (when MULTIPLE
was the default) add the following line to the control file.
set multiple_records 1
Parallel jobs in Loki
There is no support for running an individual Loki job in parallel.
However, there it is quite possible to run different jobs on different
machines (or on different processors on the same machine) in parallel. This
is use in genome screen analyses where different chromosomes or different
traits can be analyzed in parallel. The important point to remember is that
each loki run *must* be in a separate directory.
It is often useful to run a single job multiple times with different random
number seeds to verify that the results are consistent across runs. If the
runs are performed sequentially then this is OK, because Loki will start
each new run, continuing the random number stream from where it finished.
Each run will therefore get a different stream of random numbers. However,
if the jobs are run in parallel there is a risk that the random number
streams may overlap, leading to correlation between the runs. This
correlation may or may not lead to correlation between the results from the
runs.
To avoid this, Loki has multiple independent random number generators. Each
generator has the same period (2^19937). To switch from one generator to
another it is necessary to add the following line to the parameter file:
set rng x
where x is an integer between 0 and 60 (this upper limit will increase as
more independent generators are found). The generator used is written to
the seedfile, so be default subsequent runs will continue with the same
generator. Note that RNG 0 is the default generator, which was used by
previous versions of Loki. There is no guarantee that RNG 0 is independent
to all of the other generators, so it is safest to only use values of x>0
when parallel runs are performed.
In conclusion, when performing parallel runs, each run should be run in a
separate directory, and each run should be using a different random number
generator.
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1 * * * * * * * *
2 * * * * * * * *
2 * * * * * * * *
4 1 2 * * * * * *
5 1 2 * * * * * *
6 * * 1.32 * * * * 1
7 1 2 * * * * * *
8 * * 0.65 * * * * 2
9 3 4 0.32 A C * * 1
10 5 6 * * * * * *
11 5 6 1.72 C D 112 116 1
12 7 8 2.01 B C 118 118 2
13 9 10 0.90 * * 118 116 1
14 11 12 0.91 C D 118 112 1
15 13 14 1.01 C C 118 116 2
4 1 2
5 1 2
6 * * 1.32
7 1 2
8 * * 0.65
9 3 4 0.32 A C
10 5 6
11 5 6 1.72 C D 112 116
12 7 8 2.01 B C 118 118
13 9 10 0.90 * * 118 116
14 11 12 0.91 C D 118 112
15 13 14 1.01 C C 118 116
loki for Debian
---------------
Please note that loki is dead upstream, that means the development has
stopped and even the homepage http://loki.homeunix.net/ is not available any more.
You can read the content of the old homepage in the web archive at
http://web.archive.org/web/20051220050931/http://loki.homeunix.net/
If you want to download the original source tarball, try the bzipped
version (the link to the gzipped version is broken).
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.
The package "loki-doc" contains full documentation for Loki.
-- Carleos Artime <carleos@uniovi.es>, 2004-09-24
loki (2.4.7.4-6) unstable; urgency=medium
* cme fix dpkg-control
* apply install target only for architecture dependent target
Closes: #806070
* Add DEP3 header
* DEP5 fix
-- Andreas Tille <tille@debian.org> Tue, 24 Nov 2015 19:34:27 +0100
loki (2.4.7.4-5) unstable; urgency=low
* debian/upstream: added citation information
* debian/control:
- Standards-Version: 3.9.4 (no changes needed)
- cme fix dpkg-control
- Fixed Vcs fields
- Depends: ${misc:Depends}
- Canonical Vcs URLs
- Removed Homepage field since homepage vanished from the net
* debian/source/format: 3.0 (quilt)
* debian/copyright: DEP5
* debian/rules: switch from cdbs to dh
* debhelper 9 to enable hardening flags
* debian/patches/hardening.patch
-- Andreas Tille <tille@debian.org> Mon, 28 Oct 2013 17:08:17 +0100
loki (2.4.7.4-4) unstable; urgency=low
* Fixed lokisrc/param_lex.l and regenerated C file to solve problem
with redefined __unused on 64 bit systems (Thanks to brian m. carlson
<sandals@crustytoothpaste.ath.cx>)
Closes: #409370
-- Andreas Tille <tille@debian.org> Tue, 25 Mar 2008 15:14:26 +0100
loki (2.4.7.4-3) unstable; urgency=low
* Fixed install target to install to debian/tmp correctly
Closes: #472320
-- Andreas Tille <tille@debian.org> Sun, 23 Mar 2008 18:32:22 +0100
loki (2.4.7.4-2) unstable; urgency=low
* Debhelper 5
* Standards-Version: 3.7.3 (no changes necessary)
* Switch to cdbs
* Use quilt and patches
* Removed [Biology] from short description
* Added hint to long description that the project is dead
and homepage vanished
* Group maintenance according to Debian-Med policy
* Added Vcs-Fields
* Added Homepage tag (with download page of latest upstream source,
upstream seems to be dead since 1995)
* Removed watch file because project is dead upstream so watch
makes no sense
* Use a single manpage and symlinks instead of several copies of the
very same manpage file
* Remove menu entry that just calls man loki
* Fixed Section in doc-base files
* Moced doc package to section doc (as suggested by lintian)
-- Andreas Tille <tille@debian.org> Thu, 20 Mar 2008 14:39:11 +0100
loki (2.4.7.4-1) unstable; urgency=low
* New upstream release
closes: #254166
* Added a hint about loki-doc package in README.Debian.
* Standards-Version: 3.6.1
-- Carleos Artime <carleos@uniovi.es> Fri, 24 Sep 2004 15:15:27 +0000
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@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@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@pinon.ccu.uniovi.es> Sat, 5 Apr 2003 18:56:57 +0200
Source: loki
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>,
Carleos Artime <carleos@uniovi.es>
Section: science
Priority: optional
Build-Depends: debhelper (>= 9)
Standards-Version: 3.9.6
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/loki/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/loki/trunk/
Package: loki
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends}
Suggests: loki-doc
Description: 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.
Package: loki-doc
Architecture: all
Section: doc
Depends: ${misc:Depends}
Enhances: loki
Description: MCMC linkage analysis on general pedigrees (PS manual)
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.
.
Documentation on how to use Simon Heath's "prep" and "loki" tools
for MCMC genetic linkage and IBD analysis on general pedigrees.
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: Loki
Upstream-Contact: Simon C. Heath <heath@cng.fr>
Source: http://web.archive.org/web/20051220050931/http://loki.homeunix.net/
(web archive because original page vanished)
Files: *
Copyright: 1997-2004 Simon C. Heath <heath@cng.fr>
License: BSD-2-clause
Files: debian/*
Copyright: 2003-2004 Carleos Artime <carleos@uniovi.es>
2008-2012 Andreas Tille <tille@debian.org>
License: BSD-2-clause
License: BSD-2-clause
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.
This is the documentation for the loki package. The source package
of loki also contains the LaTeX source of these PostScript files.
Document: lokifaq
Title: Loki Manual
Author: Simon C. Heath
Abstract: This document answers frequently
asked questions about Loki.