For more information about GenomeTools you can visit GenomeTools homepage.
To use GenomeTools on HPC systems, you need to set up the GenomeTools environment first using the following command
source /usr/local/apps/genometools/genometools-centos7.shBelow is a simple sample run script that demonstrates the use.
#!/bin/bash #BSUB -n 1 #BSUB -W 120 #BSUB -o outLog.%J #BSUB -e errLog.%J source /usr/local/apps/genometools/genometools-centos7.sh <GenomeTools command>You need to replace <GenomeTools command> with your actual GenomeTools command. The usage for a GenomeTools command is:
gt [option ...] [tool | script] [argument ...]The following steps will walk you through an example:
cp /usr/local/apps/samples/genometools.tar .Now you should have the file genometools.tar in your working directory. To untar the file, type the command:
tar xvf genometools.tarNow you should see a list of scripts (valid_file and invalid_file) and input files (input.gff3 and invalid.gff3) needed to run the example job. First, we will submit a job that tries to validate an invalid gff3 file. Use the command:
bsub < invalid_fileUpon viewing the associated error and output files for this job, you can see that the input was not valid. The second job we will submits is a job that validates a valid gff3 file. Use the command:
bsub < valid_fileUpon viewing the associated error and output files for this job, you can see that the input was valid.
In the script, the
#BSUB -W 120means that the time limit (Wall time) set for the job is 120 minutes. You need to change that to a number that you expect as the upper time limit for your job.
In the script, the
#BSUB -o outLog.%J #BSUB -e errLog.%Jset the files that will contain standard output and standard errors, where "%J" will be the LSF job ID number when the files are finally generated. The error file may be empty if there are no errors at all in running your job.
Last modified: February 21 2024 11:48:41.