Difference between revisions of "Stacks"

Revision as of 20:44, 12 August 2022

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

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]][[Category:NGS]]
+[[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:NGS]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|stacks}}
@@ Line 20: / Line 20: @@
 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-->
-==Required Modules==
+==Environment Modules==
-[[Modules|modules documentation]]
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-===Serial===
-*{{#var:app}}
 ==System Variables==
-* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 <!--Additional-->
 {{#if: {{#var: exe}}|==Additional Information==
-The command line pipeline is available via the "stacks" module.
+The command line pipeline is available via the "stacks" environment module.
-The web interface that can be used for visualizing genetic maps and correcting the analysis is being installed and tested as of Aug 21st, 2012.
+===Database Policy===
+See [[Database_Removal_Procedure|the Database Removal Procedure]] for details on how application databases are removed or retained by UFRC.
-To run stacks with database export:
+==Running Stacks at UFRC==
-* Log into a test node and load the stacks module:
+* Log into a dev node and load the stacks module:
-* Create a database with a name that ends with "_radtags" using the 'hpc_create_stacks_db' script
+* Create a database with a name that starts with <code>"stacks_${USER}_" using the 'hpc_create_stacks_db' script
-  hpc_create_stacks_db test1_radtags
+For example:
+ hpc_create_stacks_db "stacks_${USER}_mytest1"
+The $USER variable will be expaned to your username. This will help us determine who a database belongs to if there is an issue or when we're cleaning up the old databases. Make sure to use the double quotes. Of course, you can explicitly provide a database name like
+  hpc_create_stacks_db stacks_jdoe_project21
 The script will produce an error and quit if the database already exists.
-* Log out of the test node.
-* Run 'denovo_map.pl' as usual via a batch job specifying the database name with "-B test1_radtags".
+Use the ''<tt>'hpc_list_stacks_databases [keyword]'</tt>'' command with or without a search keyword. If there is no keyword the command will list all stacks databases. If a search keyword is provided the command will list only databases containing that keyword in their name.
-* Browse to [http://stacks.hpc.ufl.edu stacks.hpc.ufl.edu] and use your HPC credentials to log in and view the results. The exact URI is constructed as follows:
-  http://stacks.hpc.ufl.edu/stacks/index.php?db=DATABASE
+For example:
-Substitute your own database name for 'DATABASE' at the end of the URI. To see an example view - go to [http://stacks.hpc.ufl.edu/index.php?db=tut_radtags http://stacks.hpc.ufl.edu/index.php?db=tut_radtags] for the output of a [http://creskolab.uoregon.edu/stacks/tut.php#pipe Stacks Tutorial].
+ hpc_list_stacks_databases test
+To delete a stacks database use the ''<tt>'hpc_remove_stacks_database [database]'</tt>'' command and provide the name of the database you want to delete as an argument.
+* Log out of the dev node.
+* Run 'denovo_map.pl' as usual via a batch job specifying the database name with "-B stacks_${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 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:
+  <nowiki>http://stacks.rc.ufl.edu/1.24/stacks/index.php?db=DATABASE</nowiki>
+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
 |}}
 <!--Configuration-->