ReadSeq
Overview
ReadSeq reads and reformats biosequences.
Setup
There is no setup needed for this software package.
Usage
ReadSeq is a Java application and as such needs to be run with the
java command. The general syntax is:
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java -cp /usr/global/readseq/readseq.jar run [options] input-file(s)
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Examples
The following is an example PBS script to run a ReadSeq job on LION-XE for a
maximum of 2 hours. It reads a FASTA-formatted input file input.fa in the
directory /home/foo/readseq and creates an XML-formatted output file
output.xml.
#PBS -l nodes=1:ppn=1
#PBS -l walltime=2:00:00
#PBS -j oe
#PBS -q lionxe-serial
# change the current working directory to the directory where
# the input file can be found
cd /home/foo/readseq
# run the ReadSeq command
java -cp /usr/global/readseq/readseq.jar run -f=xml -o=output.xml input.fa
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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
To see basic ReadSeq help, use the command:
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java -cp /usr/global/readseq/readseq.jar help
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To see more detailed ReadSeq help, use the command:
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java -cp /usr/global/readseq/readseq.jar help more
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Please send questions or suggestions about this web page to beatnic@aset.psu.edu
ASET | ITS | Penn State
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