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, 16:39, 3 March 2015
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| == Creating a New BAM Processing Pipeline == | | == Creating a New BAM Processing Pipeline == |
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| GotCloud allows you to configure new basic BAM processing pipelines via configuration. | | GotCloud allows you to configure new basic BAM processing pipelines via configuration. |
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| + | To define new processing pipelines, you will use Configuration sections to define both the pipeline and each of the steps. So first you need to understand how configuration sections work. |
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| + | === GotCloud Configuration Sections === |
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| + | |
| + | GotCloud configuration files can be broken into sections: |
| + | * Section names are specified between square brakets (<code>[]</code>) |
| + | *: <pre>[sectionName]</pre> |
| + | ** Any configuration settings specified after the section header belong to that section |
| + | ** A section can be specified multiple times in the file and the configuration settings are accumulated |
| + | ** To access a value for a key defined in another section, use <code>$(otherSectionName/keyName)</code> |
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| + | |
| + | * If a section is not specified, the configuration settings belong to the <code>global</code> section |
| + | ** The <code>global</code> section does not need to be specified at the beginning of the file (it is the default section). |
| + | ** Additional <code>global</code> settings can be set later in the file after other settings, by defining the explicitly section: |
| + | **: <pre>[global]</pre> |
| + | |
| + | |
| + | * Sections can be derived from another section |
| + | ** All sections automatically derive from <code>[global]</code> |
| + | ** A derived section inherits all the configuration settings from its parent sections |
| + | *** Parent settings are overridden by redefining the configuration key/value pair |
| + | ** A parent section is specified following a semicolon <code>:</code> on the section definition line: |
| + | **: <pre>[childSectionName] : parentSectionName</pre> |
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| + | |
| + | <ul> |
| + | <li> Section specific configuration settings are specified on the lines following the section definition: |
| + | <dd><pre>[section1] |
| + | KEY1 = VAL1 |
| + | KEY2 = VAL2 |
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| + | [section2] |
| + | KEY1 = VAL1_2 |
| + | KEY3 = VAL3</pre></dd> |
| + | </li> |
| + | </ul> |
| + | === Defining a New Pipeline === |
| # Define a new configuration section for your pipeline | | # Define a new configuration section for your pipeline |
| #: <code>[pipelineName]</code> | | #: <code>[pipelineName]</code> |