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GotCloud: GenomeSTRiP Pipeline

5,353 bytes added, 18:47, 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:
'''Replace the specified paths to the path to these files.'''
 
==GotCloud/GenomeSTRiP Command-line Options/Configuration Settings==
 
=== Required Options ===
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
! Command-line Flag !! Configuration Key !! Value Description !! Default Value
|-
| --outdir ''path'' || OUT_DIR || output directory ||
|-
| --list ''file'' || BAM_LIST || path to the [[GotCloud: Variant Calling Pipeline#BAM List File|BAM List File]] || $(OUT_DIR)/bam.list
|-
| --numjobs ''#'' || || number of jobs to run in parallel || 0 (generate Makefile of steps, but do not run)
|}
 
=== Common Options ===
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
! colspan="4" | Common Options
|-
! Command-line Flag !! Configuration Key !! Value Description !! Default Value
|-
| --conf ''file'' || || configuration file to use ||
|}
 
=== Cluster Options ===
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
! Command-line Flag !! Configuration Key !! Value Description !! Default Value
|-
| --mosix-opt ''opts'' || GENOMESTRIP_MOSIX_OPT || options to pass to the mosix command ||
|-
|}
 
=== Test/Debug Options ===
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
|-
! Command-line Flag !! Configuration Key !! Value Description !! Default Value
|-
| --verbose || || Add additional messages when reading configuration ||
|}
 
===Reference/Resource Files===
* See [[GotCloud: Genetic Reference and Resource Files]] for reference/resource file configuration settings
 
=== Analysis Region Options ===
See [[#Targeted/Exome Sequencing Settings|Targeted/Exome Sequencing Settings]] for more information on specifying exome/targetted regions and other settings.
 
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
! Command-line Flag !! Configuration Key !! Value Description !! Default Value
|-
| --chrs ''# #'' || CHRS || space separated list of chromosomes to process || 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X
|-
| --region ''#:#-#'' || GENOMESTRIP_REGION || call region - skip regions of chromosome outside of specified region
format (-end is optional): chr:start-end
|
|-
|}
 
=== Path Options ===
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
|-
! Command-line Flag !! Configuration Key !! Value Description !! Default Value
|-
| --bam-prefix ''prefix'' || BAM_PREFIX || path to prepend to relative BAM file paths in the BAM list ||
|-
| --ref-prefix ''prefix'' || REF_PREFIX || path to prepend to relative reference/resource file paths ||
|-
| --base-prefix ''prefix'' || BASE_PREFIX || path to prepend to relative paths for the BAM list file, BAM (if BAM_PREFIX isn't specified), reference/resource files (if REF_PREFIX isn't specified) ||
|-
| --gotcloudroot ''path'' || GOTCLOUD_ROOT || specify to use a different directory for finding GotCloud bins/scripts || based on the location of the gotcloud/umake.pl script
|-
|}
 
== Running GotCloud/GenomeSTRiP ==