3,045
edits
Changes
From Genome Analysis Wiki
→Configuration File
=== Configuration File ===
* 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 ==
