Difference between revisions of "Stacks"
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| − | [[Category:Software]][[Category: | + | [[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--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | |||
| − | |||
==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
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==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: | ||
| − | * Create a database with a name that starts with <code>"stacks_${USER}_" using the 'hpc_create_stacks_db' script | + | * Create a database with a name that starts with <code>"stacks_${USER}_"</code> using the 'hpc_create_stacks_db' script |
For example: | For example: | ||
| − | + | *<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 $USER variable will be expaned to your username. This will help us determine who a database belongs to if there is an issue or when we're cleaning up the old databases. Make sure to use the double quotes. Of course, you can explicitly provide a database name like | ||
| − | + | *<pre>hpc_create_stacks_db stacks_jdoe_project21</pre> | |
The script will produce an error and quit if the database already exists. | The script will produce an error and quit if the database already exists. | ||
| − | Use the ''<tt>'hpc_list_stacks_databases [keyword]'</tt>'' command with or without a search keyword. If there is no keyword the command will list all stacks databases. If a search keyword is provided the command will list only databases containing that keyword in their name. | + | Use the ''<tt>'hpc_list_stacks_databases [keyword]'</tt>'' command with or without a search keyword. If there is no keyword the command will list all stacks databases. If a search keyword is provided the command will list only databases containing that keyword in their name. For example: |
| − | + | *<pre>hpc_list_stacks_databases test</pre> | |
| − | For example: | ||
| − | |||
To delete a stacks database use the ''<tt>'hpc_remove_stacks_database [database]'</tt>'' command and provide the name of the database you want to delete as an argument. | To delete a stacks database use the ''<tt>'hpc_remove_stacks_database [database]'</tt>'' command and provide the name of the database you want to delete as an argument. | ||
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* Run 'denovo_map.pl' as usual via a batch job specifying the database name with "-B stacks_${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/$version/stacks''' e.g. [http://stacks.rc.ufl.edu/1.24/stacks http://stacks.rc.ufl.edu/1.24/stacks] and use your HPC credentials to log in and view the results. The exact URI is constructed as follows: | ||
| − | + | **<pre>http://stacks.rc.ufl.edu/1.24/stacks/index.php?db=DATABASE</pre> | |
Substitute your own database name for 'DATABASE' at the end of the URI. | Substitute your own database name for 'DATABASE' at the end of the URI. | ||
* '''New:''' Use the 'hpc_show_database_url' script to construct the URL you can use to browse to your results database. For example, | * '''New:''' Use the 'hpc_show_database_url' script to construct the URL you can use to browse to your results database. For example, | ||
| − | + | **<pre>$ hpc_show_database_url stacks_malex_test_124</pre> | |
| − | + | <br> | |
| − | + | 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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|}} | |}} | ||
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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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Latest revision as of 21:20, 2 January 2023
Description
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