Funannotate-Sapelo2: Difference between revisions
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* 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. | * 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: | To use this version of Funannotate, please follow these setup steps in your current working directory: | ||
<pre class="gscript"> | <pre class="gscript"> | ||
cp /apps/singularity-images/funannotate-1.8.17-MySQL-PASA/*.sh . | |||
cp -r /apps/singularity-images/funannotate-1.8.17-MySQL-PASA/pasa_conf . | |||
</pre> | |||
Running the first cp command above will copy three config scripts 1_init.sh, 2_create_user_and_db.sh, and 3_cleanup.sh to your current working directory. | |||
Running the second cp command above will copy a sample job submission script sub.sh to your current working directory. | |||
Below is the sample job submission script sub.sh, to run a batch job using 80 CPU cores on the batch partition: | |||
<div class="gscript2"> | <div class="gscript2"> | ||
<nowiki>#</nowiki>!/bin/bash<br> | <nowiki>#</nowiki>!/bin/bash<br> | ||
<nowiki>#</nowiki>SBATCH --job-name= | <nowiki>#</nowiki>SBATCH --job-name=<br> | ||
<nowiki>#</nowiki>SBATCH --partition=batch<br> | <nowiki>#</nowiki>SBATCH --partition=batch<br> | ||
<nowiki>#</nowiki>SBATCH --mail-type=ALL<br> | <nowiki>#</nowiki>SBATCH --mail-type=ALL<br> | ||
<nowiki>#</nowiki>SBATCH --mail-user=<u>username@uga.edu</u><br> | <nowiki>#</nowiki>SBATCH --mail-user=<u>username@uga.edu</u><br> | ||
<nowiki>#</nowiki>SBATCH --ntasks=<u>1</u><br> | <nowiki>#</nowiki>SBATCH --ntasks=<u>1</u><br> | ||
<nowiki>#</nowiki>SBATCH --mem=<u> | <nowiki>#</nowiki>SBATCH --mem=<u>80gb</u><br> | ||
<nowiki>#</nowiki>SBATCH --time=<u> | <nowiki>#</nowiki>SBATCH --time=<u>48:00:00</u><br> | ||
<nowiki>#</nowiki>SBATCH --output= | <nowiki>#</nowiki>SBATCH --output=log.%j<br> | ||
cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
Revision as of 11:25, 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 in your current working directory:
cp /apps/singularity-images/funannotate-1.8.17-MySQL-PASA/*.sh . cp -r /apps/singularity-images/funannotate-1.8.17-MySQL-PASA/pasa_conf .
Running the first cp command above will copy three config scripts 1_init.sh, 2_create_user_and_db.sh, and 3_cleanup.sh to your current working directory. Running the second cp command above will copy a sample job submission script sub.sh to your current working directory.
Below is the sample job submission script sub.sh, to run a batch job using 80 CPU cores on the batch partition:
#!/bin/bash
#SBATCH --job-name=
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=80gb
#SBATCH --time=48:00:00
#SBATCH --output=log.%j
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