GeneMachine
Overview
GeneMachine is an integrated tool intended to perform both comparative
and predictive gene identification techniques in a single run. It has
the ability to use Grail, FGENES, genscan, HMMGene, sputnik, RepeatMasker,
mzef, and BLAST in a single run. Grail and FGENES are not supported on
the LION-XE cluster.
Setup
To use GeneMachine it is necessary to set your GeneMachine environment by
running a special command once per login session. You may optionally
place these commands in your .cshrc (C Shell users) or .profile (Bourne
Shell users) to avoid having to manually run these commands on login.
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For csh and tcsh:
source /usr/local/setup/genemachine.setup.csh
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For sh and bash:
. /usr/local/setup/genemachine.setup.sh
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Usage
GeneMachine is invoked with the command genemachine. It takes an input
file in FASTA format and outputs a file readable by Sequin. Options to
the genemachine command can be seen by running genemachine --help.
Examples
The following is an example PBS script to run a GeneMachine job on LION-XE
for a maximum of 2 hours. The input file is a FASTA format file called
input.fa and is in /home/foo/genemachine. Output is specified to go to
the file genemachine.out.
#PBS -l nodes=1:ppn=2
#PBS -l walltime=2:00:00
#PBS -j oe
#PBS -q lionxe-serial
# setup the GeneMachine environment
. /usr/local/setup/genemachine.setup.sh
# change the current working directory to the directory where
# the input file input.fa can be found
cd /home/foo/genemachine
genemachine -i input.fa -o genemachine.out
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Further information on PBS scripts and submitting jobs on the LION-XE cluster
can be found in the User Guides section of the HPC website.
Documentation
Information on Genemachine syntax can be found by running the command
genemachine --help.
Please send questions or suggestions about this web page to beatnic@aset.psu.edu
ASET | ITS | Penn State
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