SNAP-Zoe-Teaching: Difference between revisions
No edit summary |
No edit summary |
||
| Line 44: | Line 44: | ||
cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
ml SNAP-Zoe/20060728-foss-2016b<br> | ml SNAP-Zoe/20060728-foss-2016b<br> | ||
snap <u>[options]</u><br> | |||
</div> | </div> | ||
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values. | In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values. | ||
| Line 50: | Line 50: | ||
Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster. | Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | 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: | |||
<pre class="gscript"> | |||
snap $ZOE/thale $EBROOTSNAPMINKORF/DNA/thale.dna.gz | |||
</pre> | |||
Here is an example of job submission command: | Here is an example of job submission command: | ||
Revision as of 15:37, 10 August 2018
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