Changes

From Genome Analysis Wiki
Jump to: navigation, search

GotCloud: GenomeSTRiP Pipeline

2,006 bytes added, 17:47, 10 February 2015
Configuration File
=== Configuration File ===
{{:The GotCloud: Configuration}}configuration file contains the run-time options, including software binaries and command line arguments. A default configuration file is automatically loaded. Users may specify their own configuration file specifying just the values different than the defaults. The configuration file is not required if there are no values to override.
* Default GotCloud configuration file is <code>gotcloud/bin/gotcloudDefaults.conf</code>
* Comments begin with a <code>#</code>
* Format: <code>KEY = value </code>
** where <code>KEY</code> is the item being set and <code>value</code> is its new value
* Some settings can be defined both in the configuration file and on the GotCloud command-line
** command-line options take priority over configuration file settings
* A KEY can be used in another KEY's value by specifying $(KEY)
** Example:
**: <code>KEY1 = value1</code>
**: <code>KEY2 = $(KEY1)/value2</code>
*** When <code>KEY2</code> is used, it will be equal to: <code>value1/value2</code>
 
====Output Directory====
* The output directory is required for running GotCloud, so GotCloud knows where to write its output
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
! Configuration Key !! Command-line Flag !! colspan="3"|Value Description
|-
|OUT_DIR||--outdir || output directory
|}
 
====Reference/Resource Files====
* See [[GotCloud: Genetic Reference and Resource Files]] for reference/resource file configuration settings
 
====Cluster Configuration====
Currently GotCloud/GenomeSTRiP only supports mosix and will wait for each job to complete after launching it.
 
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
! Configuration Key !! Command-line Flag !! colspan="3"|Value Description
|-
| GENOMESTRIP_MOSIX_OPT || --mosix-opt || colspan="3"| options to pass to mosix, example:
<pre>-j36,37,38,39,40,41,45,46,47,48,49</pre>
|}
==== GenomeSTRiP specific configuration settings ====
When using GenomeSTRiP, you need to specify the following configuration settings:

Navigation menu