Funannotate-Sapelo2 - Revision history

Shtsai at 00:39, 5 April 2026

2026-04-05T00:39:01Z

← Older revision		Revision as of 20:39, 4 April 2026
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	[[Category:~~Teaching~~]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==

	Bioinformatics		Bioinformatics

	=== Program On ===		== Program On ==

	Sapelo2		Sapelo2

	=== Version ===		== Version ==
	1.8.17		1.8.17

	=== Author / Distributor ===		== Author / Distributor ==

	https://github.com/nextgenusfs/funannotate		https://github.com/nextgenusfs/funannotate
	https://funannotate.readthedocs.io/en/latest/		https://funannotate.readthedocs.io/en/latest/

	=== 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/

	=== Running Program ===		== 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.		* 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.
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	</pre>		</pre>

	=== Documentation ===		== Documentation ==

	<pre class="gcommand">		<pre class="gcommand">
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	=== Installation ===		== Installation ==

	Source code is obtained from https://github.com/nextgenusfs/funannotate		Source code is obtained from https://github.com/nextgenusfs/funannotate

	=== System ===		== System ==
	64-bit Linux		64-bit Linux

Jordan: /* Running Program */

2026-01-14T18:27:28Z

Running Program

← Older revision		Revision as of 14:27, 14 January 2026
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	</div>		</div>

	'''~~Note~~:'''		'''Notes:'''
			# Funannotate uses the GeneMark gene prediction software, which means you need to have downloaded the key file for GeneMarker and put it into your home directory. Please follow instructions found at <u>[[GeneMarkES-Sapelo2]]</u>.
	# 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, 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.		# In the real submission script, the above the funannotate command lines in '''bold font''' can be replaced by your own funannotate command lines.

Moses at 13:47, 5 June 2025

2025-06-05T13:47:22Z

← Older revision		Revision as of 09:47, 5 June 2025
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	<nowiki>#</nowiki> Initialize and start MySQL in the container		<nowiki>#</nowiki> Initialize and start MySQL from inside of the container

	./1_init.sh && ./2_create_user_and_db.sh		./1_init.sh && ./2_create_user_and_db.sh

Moses: /* Running Program */

2025-06-05T13:25:06Z

Running Program

← Older revision		Revision as of 09:25, 5 June 2025
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	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:		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:

	<pre class="gscript">		<pre class="gscript">

Moses: /* Description */

2025-02-14T14:32:35Z

Description

← Older revision		Revision as of 10:32, 14 February 2025
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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/

Moses at 17:18, 12 February 2025

2025-02-12T17:18:02Z

← Older revision		Revision as of 13:18, 12 February 2025
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	* Three MySQL config scripts: '''1_init.sh''', '''2_create_user_and_db.sh''', and '''3_cleanup.sh'''		* 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 sample batch job submission script: '''sub.sh'''
	* A PASA config folder: '''pasa_conf/'''		* A PASA config folder: '''pasa_conf/'''

	Below is the sample job submission script sub.sh, to run a batch job using 80 CPU cores on the batch partition:		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">

Moses at 17:15, 12 February 2025

2025-02-12T17:15:52Z

← Older revision		Revision as of 13:15, 12 February 2025
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	Note:		Note:

	# Running the ~~first~~ cp ~~command above~~ will copy ~~three~~ MySQL config scripts: '''1_init.sh''', '''2_create_user_and_db.sh''', and '''3_cleanup.sh''' ~~to your current~~ job ~~working directory. It will also copy a PASA config folder~~ '''~~pasa_conf~~''' ~~to your current location.~~		Running the above cp commands will copy the following setup files and folder to your current job working directory:
	~~# Running the second cp command above will copy a sample job submission script~~ '''~~sub.sh~~''' ~~to your current 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 job submission script sub.sh, to run a batch job using 80 CPU cores on the batch partition:		Below is the sample job submission script sub.sh, to run a batch job using 80 CPU cores on the batch partition:

Moses at 17:11, 12 February 2025

2025-02-12T17:11:43Z

← Older revision		Revision as of 13:11, 12 February 2025
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	# Running the first cp command above will copy three MySQL config scripts: '''1_init.sh''', '''2_create_user_and_db.sh''', and '''3_cleanup.sh''' to your current job working directory. It will also copy a PASA config folder '''pasa_conf''' to your current location.		# Running the first cp command above will copy three MySQL config scripts: '''1_init.sh''', '''2_create_user_and_db.sh''', and '''3_cleanup.sh''' to your current job working directory. It will also copy a PASA config folder '''pasa_conf''' to your current location.
	# Running the second cp command above will copy a sample job submission script '''sub.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:		Below is the sample job submission script sub.sh, to run a batch job using 80 CPU cores on the batch partition:
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	# 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, 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.		# 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.

Moses at 17:11, 12 February 2025

2025-02-12T17:11:25Z

← Older revision		Revision as of 13:11, 12 February 2025
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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 in a batch job, please follow these setup steps in your current job working directory before submitting a batch job:~~

	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:		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:
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	</pre>		</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.		Note:
	Running the second cp command above will copy a sample job submission script sub.sh to your current working directory.
			# Running the first cp command above will copy three MySQL config scripts: '''1_init.sh''', '''2_create_user_and_db.sh''', and '''3_cleanup.sh''' to your current job working directory. It will also copy a PASA config folder '''pasa_conf''' to your current location.
			# 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:		Below is the sample job submission script sub.sh, to run a batch job using 80 CPU cores on the batch partition:

Moses at 17:07, 12 February 2025

2025-02-12T17:07:34Z

← Older revision		Revision as of 13:07, 12 February 2025
Line 23:		Line 23:

	* 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 in a batch job, please follow these setup steps in your current job working directory before submitting a batch job:

	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:		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">