Funannotate-Sapelo2: Difference between revisions
(Created page with "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 1.8.17 === Author / Distributor === https://github.com/nextgenusfs/funannotate https://funannotate.readthedocs.io/en/latest/ === Description === "Funannotate is a genome prediction, annotation, and comparison software package. It was originally written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes), but...") |
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=== Running Program === | === Running Program === | ||
* version 1.8.17 with MySQL supported PASA pipeline is installed as an Apptainer container in /apps/singularity-images/funannotate-1.8.17-MySQL-PASA/ . The image name is funannotate-1.8.17-mysql-production.sif. | |||
To use this version, please | To use this version of Funannotate, please follow these setup steps: | ||
<pre class="gscript"> | <pre class="gscript"> | ||
</pre> | </pre> | ||
Here is an example of a shell script, sub.sh, to run on the batch queue: | Here is an example of a shell script, sub.sh, to run on the batch queue: | ||
Revision as of 10:41, 12 February 2025
Category
Bioinformatics
Program On
Sapelo2
Version
1.8.17
Author / Distributor
https://github.com/nextgenusfs/funannotate https://funannotate.readthedocs.io/en/latest/
Description
"Funannotate is a genome prediction, annotation, and comparison software package. It was originally written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes), but has evolved over time to accomodate larger genomes." More details are at https://funannotate.readthedocs.io/en/latest/
Running Program
- version 1.8.17 with MySQL supported PASA pipeline is installed as an Apptainer container in /apps/singularity-images/funannotate-1.8.17-MySQL-PASA/ . The image name is funannotate-1.8.17-mysql-production.sif.
To use this version of Funannotate, please follow these setup steps:
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_HISAT2
#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=HISAT2.%j.out
#SBATCH --error=HISAT2.%j.err
cd $SLURM_SUBMIT_DIR
ml HISAT2/2.2.1-gompi-2022a
hisat2 [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 Sapelo2 for more information running jobs on the Sapelo2 cluster.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
Installation
Source code is obtained from HISAT2
System
64-bit Linux