Applications/Maker - Revision history

Pysdlb: /* Next Steps */

2022-11-16T10:49:33Z

‎Next Steps

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‎Navigation

Pysdlb at 16:51, 8 November 2022

2022-11-08T16:51:34Z

Pysdlb at 13:10, 24 May 2019

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Pysdlb at 14:17, 7 June 2018

2018-06-07T14:17:07Z

Pysdlb: Pysdlb moved page Maker to Applications/Maker without leaving a redirect

2017-04-19T11:00:20Z

Pysdlb moved page Maker to Applications/Maker without leaving a redirect

Pysdlb: Created page with "TOC ==Application Details== * Description: MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokary..."

2017-04-19T10:59:45Z

Created page with "__TOC__ ==Application Details== * Description: MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokary..."

New page

__TOC__

==Application Details==

* Description: MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.
* Version: 2.31.8
* Modules: maker/2.31.8
* Licence: GNU General Public License developed by the Free Software Foundation.

==Usage==

MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on seusequent runs. MAKER's inputs are minimal and its ouputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources.

Maker depends on the following modules on Viper

* module load ncbi-blast/2.4.0
* module load perl/5.24.0

These are loaded automatically with

* module load maker/2.31.8

===Non Interactive===

'''Note''': this example is done on a high memory node, usually access would be achieved with the scheduler

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

[username@c230 ~]$ module add maker/2.31.8
[username@c230 ~]$ maker --ignore_nfs_tmp

</pre>

===Interactive===

Through '''SLURM''' this would become the script:

A typical script would be:

<pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">

#!/bin/bash
#SBATCH -J maker
#SBATCH -N 1
#SBATCH --ntasks-per-node 1
#SBATCH -o out
#SBATCH -e err
#SBATCH -p highmem
#SBATCH --exclusive

module purge
module add gcc/4.9.3
module add maker/2.31.8

maker --ignore_nfs_tmp

</pre>

This is then submitted as follows:

<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ sbatch makerDEMO.job
Submitted batch job 289522
</pre>

==Further Information==

* [http://www.yandell-lab.org/software/maker.html http://www.yandell-lab.org/software/maker.html]

{|
|style="width:5%; border-width: 0" | [[File:icon_home.png]]
|style="width:95%; border-width: 0" |
* [[Main_Page|Home]]
* [[Applications|Application support]]
* [[General|General]]
* [[Training|Training]]
* [[Programming|Programming support]]
|-
|}

← Older revision		Revision as of 10:49, 16 November 2022
Line 73:		Line 73:

	* [http://www.yandell-lab.org/software/maker.html http://www.yandell-lab.org/software/maker.html]		* [http://www.yandell-lab.org/software/maker.html http://www.yandell-lab.org/software/maker.html]
−

	{{Modulepagenav}}		{{Modulepagenav}}

← Older revision		Revision as of 10:49, 16 November 2022
Line 75:		Line 75:


−	~~==Navigation==~~	+	{{Modulepagenav}}
−
−	* [[Main_Page\|Home]]
−	~~* [[Applications\|Application support]] *~~
−	* [[General\|General]]
−	* [[Programming\|Programming support]]

@@ Line 3: / Line 3: @@
 ==Application Details==
-* Description: MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.
+* Description: MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and create genome databases.
 * Version: 2.31.8
 * Modules: maker/2.31.8
@@ Line 10: / Line 10: @@
 ==Usage==
-MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on seusequent runs. MAKER's inputs are minimal and its ouputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources.
+MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on subsequent runs. MAKER's inputs are minimal and its outputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources.
 Maker depends on the following modules on Viper
@@ Line 70: / Line 70: @@
-==Further Information==
+==Next Steps==
 * [http://www.yandell-lab.org/software/maker.html http://www.yandell-lab.org/software/maker.html]

@@ Line 74: / Line 74: @@
 * [http://www.yandell-lab.org/software/maker.html http://www.yandell-lab.org/software/maker.html]
-{|
-|style="width:5%; border-width: 0" | [[File:icon_home.png]]
+==Navigation==
-|style="width:95%; border-width: 0" |
 * [[Main_Page|Home]]
-* [[Applications|Application support]]
+* [[Applications|Application support]] *
 * [[General|General]]
 * [[Programming|Programming support]]

@@ Line 14: / Line 14: @@
 Maker depends on the following modules on Viper
-* module load ncbi-blast/2.4.0
+* module add ncbi-blast/2.4.0
-* module load perl/5.24.0
+* module add perl/5.24.0
 These are loaded automatically with
-* module load maker/2.31.8
+* module add maker/2.31.8

← Older revision	Revision as of 11:00, 19 April 2017
(No difference)