Funannotate-Sapelo2: Difference between revisions
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=== Description === | === 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." | "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/ | More details are at https://funannotate.readthedocs.io/en/latest/ | ||
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* version 1.8.17 with PASA pipeline with MySQL support 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 PASA pipeline with MySQL support 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: | |||
To use this version of Funannotate in a batch job, please follow these setup steps in your current job working directory '''befor'''e submitting a batch job: | |||
<pre class="gscript"> | <pre class="gscript"> | ||
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</pre> | </pre> | ||
Note: | |||
Below is the sample job submission script sub.sh | Running the above cp commands will copy the following setup files and folder to your current job working directory: | ||
* Three MySQL config scripts: '''1_init.sh''', '''2_create_user_and_db.sh''', and '''3_cleanup.sh''' | |||
* A sample batch job submission script: '''sub.sh''' | |||
* A PASA config folder: '''pasa_conf/''' | |||
Below is the sample batch job submission script ('''sub.sh''') to run funannotate in a batch job using 80 CPU cores on the batch partition: | |||
<div class="gscript2"> | <div class="gscript2"> | ||
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<nowiki>#</nowiki>SBATCH --output=log.%j.out<br> | <nowiki>#</nowiki>SBATCH --output=log.%j.out<br> | ||
<nowiki>#</nowiki>SBATCH --mail-type=ALL<br> | <nowiki>#</nowiki>SBATCH --mail-type=ALL<br> | ||
<nowiki>#</nowiki>SBATCH --mail-user=<u>username@uga.edu | <nowiki>#</nowiki>SBATCH --mail-user=<u>username</u>@uga.edu<br> | ||
cd $SLURM_SUBMIT_DIR | cd $SLURM_SUBMIT_DIR | ||
<nowiki>#</nowiki> Initialize MySQL in container | <nowiki>#</nowiki> Initialize and start MySQL in the container | ||
./1_init.sh && ./2_create_user_and_db.sh | ./1_init.sh && ./2_create_user_and_db.sh | ||
<nowiki>#</nowiki> Verify the installation of dependencies and show their versions | <nowiki>#</nowiki> Verify the installation of dependencies and show their versions (optional) | ||
funannotate check --show-versions" | apptainer exec instance://funannotate-mysql /bin/bash -c "source activate /opt/funannotate && '''funannotate check --show-versions'''" | ||
<nowiki>#</nowiki> Run a full test with PASA pipeline with MySQL support. You can run your own funannotate command line here. | |||
funannotate test -t all --cpus 80" | apptainer exec instance://funannotate-mysql /bin/bash -c "source activate /opt/funannotate && '''funannotate test -t all --cpus 80'''" | ||
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</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. | '''Note:''' | ||
# In the real submission script, at least all the above underlined values in Slurm headers need to be reviewed or to be replaced by the proper values. | |||
# In the real submission script, the above the funannotate command lines in '''bold font''' can be replaced by your own funannotate command lines. | |||
Please refer to [[Running Jobs on Sapelo2]] for more information running jobs on the Sapelo2 cluster. | Please refer to [[Running Jobs on Sapelo2]] for more information running jobs on the Sapelo2 cluster. | ||
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=== Documentation === | === Documentation === | ||
<pre | <pre class="gcommand"> | ||
https://funannotate.readthedocs.io/en/latest/ | |||
https://github.com/PASApipeline/PASApipeline/wiki/setting-up-pasa-mysql | |||
</pre> | </pre> | ||
[[#top|Back to Top]] | [[#top|Back to Top]] | ||
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=== Installation === | === Installation === | ||
Source code is obtained from | Source code is obtained from https://github.com/nextgenusfs/funannotate | ||
=== System === | === System === | ||
64-bit Linux | 64-bit Linux | ||
Latest revision as of 09:32, 14 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 PASA pipeline with MySQL support 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 in a batch job, please follow these setup steps in your current job working directory before submitting a batch job:
cp /apps/singularity-images/funannotate-1.8.17-MySQL-PASA/*.sh . cp -r /apps/singularity-images/funannotate-1.8.17-MySQL-PASA/pasa_conf .
Note:
Running the above cp commands will copy the following setup files and folder to your current job working directory:
- Three MySQL config scripts: 1_init.sh, 2_create_user_and_db.sh, and 3_cleanup.sh
- A sample batch job submission script: sub.sh
- A PASA config folder: pasa_conf/
Below is the sample batch job submission script (sub.sh) to run funannotate in a batch job using 80 CPU cores on the batch partition:
#!/bin/bash
#SBATCH --job-name=funannotate-mysql
#SBATCH --partition=batch
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=80
#SBATCH --mem=80gb
#SBATCH --time=48:00:00
#SBATCH --output=log.%j.out
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
cd $SLURM_SUBMIT_DIR
# Initialize and start MySQL in the container
./1_init.sh && ./2_create_user_and_db.sh
# Verify the installation of dependencies and show their versions (optional)
apptainer exec instance://funannotate-mysql /bin/bash -c "source activate /opt/funannotate && funannotate check --show-versions"
# Run a full test with PASA pipeline with MySQL support. You can run your own funannotate command line here.
apptainer exec instance://funannotate-mysql /bin/bash -c "source activate /opt/funannotate && funannotate test -t all --cpus 80"
# Clean up on the compute node by shutting down MySQL
./3_cleanup.sh
Note:
- In the real submission script, at least all the above underlined values in Slurm headers need to be reviewed or to be replaced by the proper values.
- In the real submission script, the above the funannotate command lines in bold font can be replaced by your own funannotate command lines.
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
https://funannotate.readthedocs.io/en/latest/ https://github.com/PASApipeline/PASApipeline/wiki/setting-up-pasa-mysql
Installation
Source code is obtained from https://github.com/nextgenusfs/funannotate
System
64-bit Linux