Difference between revisions of "Stacks"

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

@@ 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}}
 |{{#vardefine:url|http://creskolab.uoregon.edu/stacks/}}
 <!--CONFIGURATION: OPTIONAL (1=ON)-->
-|{{#vardefine:mod|1}} <!--MODULES - NOW REQUIRED-->
-|{{#vardefine:intel|}} <!-- "11.1" - Compiler Module Choice -->
-|{{#vardefine:mpi|}} <!-- "openmpi/1.3.4"- MPI Module Choice -->
 |{{#vardefine:exe|1}} <!--RUNNING -->
 |{{#vardefine:conf|}} <!--CONFIGS-->
@@ Line 19: / Line 16: @@
 <!--Description-->
 {{#if: {{#var: url}}|
-{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}
+{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 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.
-<!--Location-->
-{{App_Location|app={{#var:app}}|{{#var:ver}}}}
-<!--Versions-->
-==Available versions==
-* 0.9995
 <!--Modules-->
-{{#if: {{#var: mod}}|==Running the application using modules==
+==Environment Modules==
-{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
+==System Variables==
-<!--Run-->
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
-{{#if: {{#var: exe}}|==How To Run==
+<!--Additional-->
-The command line pipeline is available via the "stacks" module.
+{{#if: {{#var: exe}}|==Additional Information==
+The command line pipeline is available via the "stacks" environment module.
+===Database Policy===
+See [[Database_Removal_Procedure|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 <code>"stacks_${USER}_"</code> using the 'hpc_create_stacks_db' script
+For example:
+*<pre> hpc_create_stacks_db "stacks_${USER}_mytest1"</pre>
+The $USER variable will be expaned to your username. This will help us determine who a database belongs to if there is an issue or when we're cleaning up the old databases. Make sure to use the double quotes. Of course, you can explicitly provide a database name like
+*<pre>hpc_create_stacks_db stacks_jdoe_project21</pre>
+The script will produce an error and quit if the database already exists.
+Use the ''<tt>'hpc_list_stacks_databases [keyword]'</tt>'' command with or without a search keyword. If there is no keyword the command will list all stacks databases. If a search keyword is provided the command will list only databases containing that keyword in their name. For example:
+*<pre>hpc_list_stacks_databases test</pre>
-The web interface that can be used for visualizing genetic maps and correcting the analysis is not installed, but is being evaluated for installation.
+To delete a stacks database use the ''<tt>'hpc_remove_stacks_database [database]'</tt>'' command and provide the name of the database you want to delete as an argument.
+* Log out of the dev node.
+* Run 'denovo_map.pl' as usual via a batch job specifying the database name with "-B stacks_${USER}_test1".
+* Find the stacks version you ran and Browse to '''http://stacks.rc.ufl.edu/$version/stacks''' e.g.  [http://stacks.rc.ufl.edu/1.24/stacks http://stacks.rc.ufl.edu/1.24/stacks] and use your HPC credentials to log in and view the results. The exact URI is constructed as follows:
+**<pre>http://stacks.rc.ufl.edu/1.24/stacks/index.php?db=DATABASE</pre>
+Substitute your own database name for 'DATABASE' at the end of the URI.
+* '''New:''' Use the 'hpc_show_database_url' script to construct the URL you can use to browse to your results database. For example,
+**<pre>$ 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
 |}}
 <!--Configuration-->
@@ Line 44: / Line 65: @@
 See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 <!--Policy-->
-{{#if: {{#var: policy}}|==Usage policy==
+{{#if: {{#var: policy}}|==Usage Policy==
 WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)
 |}}