Fastlink on Biowulf

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Fastlink & FastSLINK on Biowulf

Genetic linkage analysis is a statistical technique used to map genes and find the approximate location of disease genes. The LINKAGE program suite was an earlier package for genetic linkage analysis. FASTLINK is a signficantly modified and improved version of the main programs of LINKAGE that run much faster sequentially, allow the user to recover gracefully from a crash, and provides new improved documentation.

The SLINK package contains a simluation program slink and backend programs unknown, msim, lsim, isim. SLINK generates random replicates, and msim, lsim, isim analyze the replicates. The FastSLINK program is the merger of code from FASTLINK version 2.x to the slink program, by Alejandro Schaffer and Dan Weeks.

FASTLINK homepage at NCBI

Fastlink and FastSLINK on Biowulf are not parallelized. The advantage of running them on Biowulf would be to run 'swarms' of single-threaded jobs, since each job is sent to a separate Biowulf node

Executables in /usr/local/bin are:
Fastlink executables: ilink, linkmap, lodscore, mlink, unknown
additional utilities: makeped, lsp, lrp, lcp
FastSLINK executables: slink, msim, lsim, isim, unknown_slink (Note: this is a different version of the unknown program that is required to for FastSLINK)

All documentation and sources are in /usr/local/linkage

Submitting a swarm job

Set up a swarm command file (e.g. /home/username/cmdfile). Here is a sample file:


cd /home/username/run1; ./infile1 > outfile1
cd /home/username/run2; ./infile2 > outfile2
cd /home/username/run3; ./infile3 > outfile3
....

where the file infile1 would contain a sequence of FASTLINK commands. This set of commands can be generated using the lcp (Linkage Control Program) command.

Submit this swarm command file to the batch system with the command:

biobos$ swarm -f cmdfile

Swarm will run 2 jobs per node, since the Biowulf nodes are all 2-processor. See the Swarm documentation for more information.

Documentation

Look at the README and doc files in /usr/local/linkage/fastlink & fastslink
Exercises in Genetic Linkage Analysis from the MRC, UK. One particularly useful section is Using the Linkage Utility programs to perform analyses.

This document is available as http://biowulf.nih.gov/apps/gaussian.html
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