SNAP-Zoe-Teaching
Category
Bioinformatics
Program On
Teaching
Version
20060728
Author / Distributor
Description
"SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser." More details are at SNAP-Zoe
Running Program
The last version of this application is at /usr/local/apps/eb/SNAP-Zoe/20060728-foss-2016b
To use this version, please load the module with
ml SNAP-Zoe/20060728-foss-2016b
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_SNAP-Zoe
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=SNAP-Zoe.%j.out
#SBATCH --error=SNAP-Zoe.%j.err
cd $SLURM_SUBMIT_DIR
ml SNAP-Zoe/20060728-foss-2016b
snap [options]
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.
Please Note: ZOE is the environment variable can be used by snap to find the HMM files storing at /usr/local/apps/eb/SNAP-Zoe/20060728-foss-2016b/HMM; EBROOTSNAPMINZOE is the environment variable storing the installation path at /usr/local/apps/eb/SNAP-Zoe/20060728-foss-2016b). For example, to run a test with a sample sequence in $EBROOTSNAPMINKORF/DNA:
snap $ZOE/thale $EBROOTSNAPMINKORF/DNA/thale.dna.gz
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
ml SNAP-Zoe/20060728-foss-2016b
Installation
Source code is obtained from SNAP-Zoe
System
64-bit Linux