IBD_Stitch
IBD_Stitch: Sequential construction of IBD states among multiple individuals
1. Overview
The ibd_stitch program constructs IBD states among multiple individuals using a
PAC (product-of-approximate-conditionals) likelihood approach.
Chris Glazner's Haskell ibd_stitch code is available from
this github site.
Latest release, June 25, 2014.
Other Glazner software relating to IBD inference
is also available on this site.
2. Installation
The following installation helpful instructions were provided by Hiep
Nguyen, December 2015.
Note that Redhat7 was needed: installation under
older Redhat versions was not possible.
Note that ``$'' below is the linux/unix prompt.
1. ibd_stitch.cabal requires GHC compiler and Cabal (a package install and
build tool)
I chose to install them with rpm packages and installed them on Redhat 7.2
64bit. The package names are:
- cabal-dev-0.9.2-1.el7.x86_64.rpm
- cabal-install-1.16.1.0-1.el7.x86_64.rpm
- ghc-XXX.rpm (approximately 50 packages)
|
|
2. Make sure gsl and gsl-devel are installed
|
|
3. Make sure lapack and lapack-devel are installed
|
4. install cabal-install, cabal-dev and happy program:
- $ cabal update
- $ cabal install cabal-install
This will create ~/.cabal/bin/cabal executable file
Then
- $ ~/.cabal/bin/cabal install cabal-dev
- $ ~/.cabal/bin/cabal install happy
These will create cabal-dev, happy, lens executable files in~/.cabal/bin/
directory
|
5. Add ~/.cabal/bin/ to your path.
For example in bash:
- $ export PATH=$PATH:~/.cabal/bin/
|
6. Compile ibd_stitch
Get ibd_stitch-master.zip from https://github.com/cglazner/ibd_stitch
-
$ unzip ibd_stitch-master.zip
This will create ibd_stitch-master directory
Then
- $ cd ibd_stitch-master
- $ ~/.cabal/bin/cabal-dev install
This will create ibd_stitch executable file for you in
ibd_stitch-master/cabal-dev/bin/
|
ibd_stitch is invoked with a single parameter file, which in
turn specifies a required marker data file. For examples of these
files, and information on running the program and interpreting the
output, please see the tutorial.
The tutorial is based on text provided
by Fiona Grimson.
The tutorial and decribed example files are also available in a
gzipped tar file.
These examples
have been tested on several operating systems, but please be aware they are
not robust. Whether due to the alternate Haskell installations, or to the
program itself, some apparently identical parameter files will not run on
some systems. It is possible the code references unitialized space, but
the problem appears to be in reading the parameter file and setting up
the logfile. In the parameter file,
some forms of white space (e.g. tab) and/or use of default file names
(you are advised to specify your logfile explicitly) can cause problems
on some systems.