GeneMarkES-Sapelo2 - Revision history

Shtsai at 00:44, 5 April 2026

2026-04-05T00:44:36Z

← Older revision		Revision as of 20:44, 4 April 2026
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	[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==

	Bioinformatics		Bioinformatics

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

	Sapelo2		Sapelo2

	=== Version ===		== Version ==
	4.71		4.71

	=== Author / Distributor ===		== Author / Distributor ==
	[http://exon.gatech.edu/GeneMark/ GeneMarkES]		[http://exon.gatech.edu/GeneMark/ GeneMarkES]

	=== Description ===		== Description ==
	"Gene Prediction in Eukaryotes. Novel genomes can be analyzed by the program GeneMark-ES utilizing unsupervised training."		"Gene Prediction in Eukaryotes. Novel genomes can be analyzed by the program GeneMark-ES utilizing unsupervised training."
	More details are at [http://exon.gatech.edu/GeneMark/ GeneMarkES]		More details are at [http://exon.gatech.edu/GeneMark/ GeneMarkES]

	=== Running Program ===		== Running Program ==

	Also refer to [[Running Jobs on Sapelo2]]		Also refer to [[Running Jobs on Sapelo2]]
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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 from [http://exon.gatech.edu/GeneMark/license_download.cgi GeneMarkES]		source code from [http://exon.gatech.edu/GeneMark/license_download.cgi GeneMarkES]

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

Jordan: /* Running Program */

2026-03-24T19:06:30Z

Running Program

← Older revision		Revision as of 15:06, 24 March 2026
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	1) Go to http://topaz.gatech.edu/GeneMark/license_download.cgi, fill the requested fields are read the license text. Note: you can select any tool and platform actually, e.g. GeneMark-ES/ET/EP+ ver 4.72_lic and LINUX64 kernel 3.10-5, but <b>make sure you select both a software option and an operating system option, otherwise the form will re-set when you enter your information and click "I agree."</b>		1) Go to http://topaz.gatech.edu/GeneMark/license_download.cgi, fill the requested fields are read the license text. Note: you can select any tool and platform actually, e.g. GeneMark-ES/ET/EP+ ver 4.72_lic and LINUX64 kernel 3.10-5, but <b>make sure you select both a software option and an operating system option, otherwise the form will re-set when you enter your information and click "I agree."</b>

	2) After pressing "I agree ..." button you will be redirected to a download page. You will need to download the 64bit key file only. The key file gm_key_64.gz will be downloaded to your local drive~~. Then please~~ transfer it to the cluster using a transfer node or Globus. Please refer to [[Transferring Files]].		2) After pressing "I agree ..." button you will be redirected to a download page. You will need to download the 64bit key file only. Here you have two options:</br>
			-A. If you're already logged into Sapelo2, you can right-click or CTRL + click on the 64-bit link and copy the URL, then 'cd' to your /home directory, type 'wget' and paste the URL into your terminal window and the key file gm_key_64.gz will be downloaded to your /home directory. Or,</br>
			-B. Click the 64-bit link in your browser. The key file gm_key_64.gz will be downloaded to your local drive, and you can then transfer it to the cluster using a transfer node or Globus. Please refer to [[Transferring Files]].

	3) The key file downloaded is in gzip format, on the cluster please unpack it (with gunzip) and move it to ~/.gm_key (the name should be exactly like this, with a dot in the beginning), for example:		3) The key file downloaded is in gzip format, on the cluster please unpack it (with gunzip) and move it to ~/.gm_key (the name should be exactly like this, with a dot in the beginning), for example:

Jordan: /* Running Program */

2026-03-24T18:16:34Z

Running Program

← Older revision		Revision as of 14:16, 24 March 2026
Line 24:		Line 24:
	In order to use geneMarker you will need to download a key file and put it into your home directory. Please follow instructions as given below:		In order to use geneMarker you will need to download a key file and put it into your home directory. Please follow instructions as given below:

	1) Go to http://topaz.gatech.edu/GeneMark/license_download.cgi, fill the requested fields are read the license text. Note: you can select any tool and platform actually, e.g. GeneMark-ES/ET/EP+ ver 4.72_lic and LINUX64 kernel 3.10-5.		1) Go to http://topaz.gatech.edu/GeneMark/license_download.cgi, fill the requested fields are read the license text. Note: you can select any tool and platform actually, e.g. GeneMark-ES/ET/EP+ ver 4.72_lic and LINUX64 kernel 3.10-5, but <b>make sure you select both a software option and an operating system option, otherwise the form will re-set when you enter your information and click "I agree."</b>

	2) After pressing "I agree ..." button you will be redirected to a download page. You will need to download the 64bit key file only. The key file gm_key_64.gz will be downloaded to your local drive. Then please transfer it to the cluster using a transfer node or Globus. Please refer to [[Transferring Files]].		2) After pressing "I agree ..." button you will be redirected to a download page. You will need to download the 64bit key file only. The key file gm_key_64.gz will be downloaded to your local drive. Then please transfer it to the cluster using a transfer node or Globus. Please refer to [[Transferring Files]].

Jordan: /* Running Program */

2025-02-24T17:23:26Z

Running Program

← Older revision		Revision as of 13:23, 24 February 2025
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	1) Go to http://topaz.gatech.edu/GeneMark/license_download.cgi, fill the requested fields are read the license text. Note: you can select any tool and platform actually, e.g. GeneMark-ES/ET/EP+ ver 4.72_lic and LINUX64 kernel 3.10-5.		1) Go to http://topaz.gatech.edu/GeneMark/license_download.cgi, fill the requested fields are read the license text. Note: you can select any tool and platform actually, e.g. GeneMark-ES/ET/EP+ ver 4.72_lic and LINUX64 kernel 3.10-5.

	2) After pressing "I agree ..." button you will be redirected to a download page. You will need to download the 64bit key file only. The key file gm_key_64.gz will be downloaded to your local drive. Then please transfer it to the cluster using a transfer node. Please refer to [[Transferring Files]].		2) After pressing "I agree ..." button you will be redirected to a download page. You will need to download the 64bit key file only. The key file gm_key_64.gz will be downloaded to your local drive. Then please transfer it to the cluster using a transfer node or Globus. Please refer to [[Transferring Files]].

	3) The key file downloaded is in gzip format, on the cluster please unpack it (with gunzip) and move it to ~/.gm_key (the name should be exactly like this, with a dot in the beginning), for example:		3) The key file downloaded is in gzip format, on the cluster please unpack it (with gunzip) and move it to ~/.gm_key (the name should be exactly like this, with a dot in the beginning), for example:

Moses: /* Running Program */

2024-06-04T16:38:42Z

Running Program

← Older revision		Revision as of 12:38, 4 June 2024
Line 24:		Line 24:
	In order to use geneMarker you will need to download a key file and put it into your home directory. Please follow instructions as given below:		In order to use geneMarker you will need to download a key file and put it into your home directory. Please follow instructions as given below:

	1) Go to http://topaz.gatech.edu/GeneMark/license_download.cgi, fill the requested fields are read the license text. Note: you can select any tool and platform actually, e.g. GeneMark-ES/ET/EP+ ver 4.~~71_lic~~ and LINUX64.		1) Go to http://topaz.gatech.edu/GeneMark/license_download.cgi, fill the requested fields are read the license text. Note: you can select any tool and platform actually, e.g. GeneMark-ES/ET/EP+ ver 4.72_lic and LINUX64 kernel 3.10-5.

	2) After pressing "I agree ..." button you will be redirected to a download page. You will need to download the 64bit key file only. The key file gm_key_64.gz will be downloaded to your local drive. Then please transfer it to the cluster using a transfer node. Please refer to [[Transferring Files]].		2) After pressing "I agree ..." button you will be redirected to a download page. You will need to download the 64bit key file only. The key file gm_key_64.gz will be downloaded to your local drive. Then please transfer it to the cluster using a transfer node. Please refer to [[Transferring Files]].

Chelsea: /* Running Program */

2024-04-10T20:29:51Z

Running Program

← Older revision		Revision as of 16:29, 10 April 2024
Line 24:		Line 24:
	In order to use geneMarker you will need to download a key file and put it into your home directory. Please follow instructions as given below:		In order to use geneMarker you will need to download a key file and put it into your home directory. Please follow instructions as given below:

	1) Go to [http://topaz.gatech.edu/GeneMark/license_download.cgi ~~http://exon.gatech.edu/GeneMark/license_download.cgi]~~, fill the requested fields are read the license text. Note: you can select any tool and platform actually, e.g. GeneMark-ES/ET/EP+ ver 4.71_lic and LINUX64.		1) Go to http://topaz.gatech.edu/GeneMark/license_download.cgi, fill the requested fields are read the license text. Note: you can select any tool and platform actually, e.g. GeneMark-ES/ET/EP+ ver 4.71_lic and LINUX64.

	2) After pressing "I agree ..." button you will be redirected to a download page. You will need to download the 64bit key file only. The key file gm_key_64.gz will be downloaded to your local drive. Then please transfer it to the cluster using a transfer node. Please refer to [[Transferring Files]].		2) After pressing "I agree ..." button you will be redirected to a download page. You will need to download the 64bit key file only. The key file gm_key_64.gz will be downloaded to your local drive. Then please transfer it to the cluster using a transfer node. Please refer to [[Transferring Files]].

Chelsea: /* Running Program */

2024-04-10T20:29:37Z

Running Program

← Older revision		Revision as of 16:29, 10 April 2024
Line 24:		Line 24:
	In order to use geneMarker you will need to download a key file and put it into your home directory. Please follow instructions as given below:		In order to use geneMarker you will need to download a key file and put it into your home directory. Please follow instructions as given below:

	1) Go to http://exon.gatech.edu/GeneMark/license_download.cgi, fill the requested fields are read the license text. Note: you can select any tool and platform actually, e.g. GeneMark-ES/ET/EP+ ver 4.71_lic and LINUX64.		1) Go to [http://topaz.gatech.edu/GeneMark/license_download.cgi http://exon.gatech.edu/GeneMark/license_download.cgi], fill the requested fields are read the license text. Note: you can select any tool and platform actually, e.g. GeneMark-ES/ET/EP+ ver 4.71_lic and LINUX64.

	2) After pressing "I agree ..." button you will be redirected to a download page. You will need to download the 64bit key file only. The key file gm_key_64.gz will be downloaded to your local drive. Then please transfer it to the cluster using a transfer node. Please refer to [[Transferring Files]].		2) After pressing "I agree ..." button you will be redirected to a download page. You will need to download the 64bit key file only. The key file gm_key_64.gz will be downloaded to your local drive. Then please transfer it to the cluster using a transfer node. Please refer to [[Transferring Files]].

Moses at 12:58, 7 September 2023

2023-09-07T12:58:09Z

← Older revision		Revision as of 08:58, 7 September 2023
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	'''Version 4.71'''		'''Version 4.71'''

	Version 4.71, installed at /apps/eb/GeneMark-ET/4.71-GCCcore-11.3.0/		Version 4.71, installed at

			* /apps/eb/GeneMark-ET/4.71-GCCcore-11.3.0/
			* /apps/eb/GeneMark-ET/4.71-GCCcore-11.2.0/

	To use it, please load the module with:		To use it, please load the module with:
	<div class="gscript2">		<div class="gscript2">
	module load GeneMark-ET/4.71-GCCcore-11.3.0		module load GeneMark-ET/4.71-GCCcore-11.3.0
			</div>

			or
			<div class="gscript2">
			module load GeneMark-ET/4.71-GCCcore-11.2.0
	</div>		</div>

Moses at 12:54, 7 September 2023

2023-09-07T12:54:02Z

Show changes

Moses at 14:54, 12 December 2022

2022-12-12T14:54:00Z

← Older revision		Revision as of 10:54, 12 December 2022
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	=== Version ===		=== Version ===
	4.57		4.57, 4.71

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