Difference between revisions of "Stacks"

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[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]][[Category:NGS]]
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[[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:NGS]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|stacks}}
 
|{{#vardefine:app|stacks}}
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Stacks is a software pipeline for building loci out of a set of short-read sequenced samples. Stacks was developed for the purpose of building genetic maps from RAD-Tag Illumina sequence data, but can also be readily applied to population studies, and phylogeography.
 
Stacks is a software pipeline for building loci out of a set of short-read sequenced samples. Stacks was developed for the purpose of building genetic maps from RAD-Tag Illumina sequence data, but can also be readily applied to population studies, and phylogeography.
 
<!--Modules-->
 
<!--Modules-->
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==Required Modules==
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==Environment Modules==
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[[Modules|modules documentation]]
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
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===Serial===
 
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*{{#var:app}}
 
 
==System Variables==
 
==System Variables==
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* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
<!--Additional-->
 
<!--Additional-->
 
{{#if: {{#var: exe}}|==Additional Information==
 
{{#if: {{#var: exe}}|==Additional Information==
 
The command line pipeline is available via the "stacks" environment module.  
 
The command line pipeline is available via the "stacks" environment module.  
  
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'''Note:''' research databases older than 3 months are not guaranteed to be retained on the research database server. Please open a [http://support.rc.ufl.edu Support Request] if you need to retain the data for a longer period of time.
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===Database Policy===
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See [[Database_Removal_Procedure|the Database Removal Procedure]] for details on how application databases are removed or retained by UFRC.
  
 
==Running Stacks at UFRC==
 
==Running Stacks at UFRC==
 
* Log into a dev node and load the stacks module:
 
* Log into a dev node and load the stacks module:
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* Create a database with a name that starts with <code>"stacks_${USER}_" using the 'hpc_create_stacks_db' script
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* Create a database with a name that starts with <code>"stacks_${USER}_"</code> using the 'hpc_create_stacks_db' script
  
 
For example:
 
For example:
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hpc_create_stacks_db "stacks_${USER}_mytest1"
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*<pre> hpc_create_stacks_db "stacks_${USER}_mytest1"</pre>
 
The $USER variable will be expaned to your username. This will help us determine who a database belongs to if there is an issue or when we're cleaning up the old databases. Make sure to use the double quotes. Of course, you can explicitly provide a database name like
 
The $USER variable will be expaned to your username. This will help us determine who a database belongs to if there is an issue or when we're cleaning up the old databases. Make sure to use the double quotes. Of course, you can explicitly provide a database name like
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hpc_create_stacks_db stacks_jdoe_project21
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*<pre>hpc_create_stacks_db stacks_jdoe_project21</pre>
 
The script will produce an error and quit if the database already exists.
 
The script will produce an error and quit if the database already exists.
  
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Use the ''<tt>'hpc_list_stacks_databases [keyword]'</tt>'' command with or without a search keyword. If there is no keyword the command will list all stacks databases. If a search keyword is provided the command will list only databases containing that keyword in their name.
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Use the ''<tt>'hpc_list_stacks_databases [keyword]'</tt>'' command with or without a search keyword. If there is no keyword the command will list all stacks databases. If a search keyword is provided the command will list only databases containing that keyword in their name. For example:
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*<pre>hpc_list_stacks_databases test</pre>
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For example:
 
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hpc_list_stacks_databases test
 
  
 
To delete a stacks database use the ''<tt>'hpc_remove_stacks_database [database]'</tt>'' command and provide the name of the database you want to delete as an argument.
 
To delete a stacks database use the ''<tt>'hpc_remove_stacks_database [database]'</tt>'' command and provide the name of the database you want to delete as an argument.
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* Run 'denovo_map.pl' as usual via a batch job specifying the database name with "-B stacks_${USER}_test1".
 
* Run 'denovo_map.pl' as usual via a batch job specifying the database name with "-B stacks_${USER}_test1".
 
* Find the stacks version you ran and Browse to '''http://stacks.rc.ufl.edu/$version/stacks''' e.g.  [http://stacks.rc.ufl.edu/1.24/stacks http://stacks.rc.ufl.edu/1.24/stacks] and use your HPC credentials to log in and view the results. The exact URI is constructed as follows:
 
* Find the stacks version you ran and Browse to '''http://stacks.rc.ufl.edu/$version/stacks''' e.g.  [http://stacks.rc.ufl.edu/1.24/stacks http://stacks.rc.ufl.edu/1.24/stacks] and use your HPC credentials to log in and view the results. The exact URI is constructed as follows:
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<nowiki>http://stacks.rc.ufl.edu/1.24/stacks/index.php?db=DATABASE</nowiki>
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**<pre>http://stacks.rc.ufl.edu/1.24/stacks/index.php?db=DATABASE</pre>
 
Substitute your own database name for 'DATABASE' at the end of the URI.
 
Substitute your own database name for 'DATABASE' at the end of the URI.
 
* '''New:''' Use the 'hpc_show_database_url' script to construct the URL you can use to browse to your results database. For example,
 
* '''New:''' Use the 'hpc_show_database_url' script to construct the URL you can use to browse to your results database. For example,
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$ hpc_show_database_url stacks_malex_test_124
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**<pre>$ hpc_show_database_url stacks_malex_test_124</pre>
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<br>
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Your results can be viewed at the following URL:
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Your results can be viewed at the following URL:
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  http://stacks.rc.ufl.edu/1.24/stacks/?db=stacks_malex_test_124
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        http://stacks.rc.ufl.edu/1.24/stacks/?db=stacks_malex_test_124
 
 
   
 
   
 
|}}
 
|}}
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See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
 
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
 
__NOTOC____NOEDITSECTION__
 
__NOTOC____NOEDITSECTION__
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=Validation=
 
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* Validate 4/5/2018
 

Latest revision as of 21:20, 2 January 2023

Description

stacks website  

Stacks is a software pipeline for building loci out of a set of short-read sequenced samples. Stacks was developed for the purpose of building genetic maps from RAD-Tag Illumina sequence data, but can also be readily applied to population studies, and phylogeography.

Environment Modules

Run module spider stacks to find out what environment modules are available for this application.

System Variables

  • HPC_STACKS_DIR - installation directory

Additional Information

The command line pipeline is available via the "stacks" environment module.

Database Policy

See the Database Removal Procedure for details on how application databases are removed or retained by UFRC.

Running Stacks at UFRC

  • Log into a dev node and load the stacks module:
  • Create a database with a name that starts with "stacks_${USER}_" using the 'hpc_create_stacks_db' script

For example: 

  •  hpc_create_stacks_db "stacks_${USER}_mytest1"

The $USER variable will be expaned to your username. This will help us determine who a database belongs to if there is an issue or when we're cleaning up the old databases. Make sure to use the double quotes. Of course, you can explicitly provide a database name like 

  • hpc_create_stacks_db stacks_jdoe_project21

The script will produce an error and quit if the database already exists.

Use the 'hpc_list_stacks_databases [keyword]' command with or without a search keyword. If there is no keyword the command will list all stacks databases. If a search keyword is provided the command will list only databases containing that keyword in their name. For example: 

  • hpc_list_stacks_databases test

To delete a stacks database use the 'hpc_remove_stacks_database [database]' command and provide the name of the database you want to delete as an argument.

  • Log out of the dev node.
  • Run 'denovo_map.pl' as usual via a batch job specifying the database name with "-B stacks_${USER}_test1".
  • Find the stacks version you ran and Browse to http://stacks.rc.ufl.edu/$version/stacks e.g. http://stacks.rc.ufl.edu/1.24/stacks and use your HPC credentials to log in and view the results. The exact URI is constructed as follows: 
    • http://stacks.rc.ufl.edu/1.24/stacks/index.php?db=DATABASE

Substitute your own database name for 'DATABASE' at the end of the URI.

  • New: Use the 'hpc_show_database_url' script to construct the URL you can use to browse to your results database. For example, 
    • $ hpc_show_database_url stacks_malex_test_124


Your results can be viewed at the following URL: 

http://stacks.rc.ufl.edu/1.24/stacks/?db=stacks_malex_test_124





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