Commit b136b581 authored by Sander Bollen's avatar Sander Bollen
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Sage documentation

parent b662fcf5
...@@ -15,10 +15,21 @@ This pipeline uses the following modules and tools: ...@@ -15,10 +15,21 @@ This pipeline uses the following modules and tools:
* [SageCreateTagCounts](../tools/sagetools.md) * [SageCreateTagCounts](../tools/sagetools.md)
## Configuration ## Configuration and flags
Note that one should first create the appropriate [configs](../general/config.md). Note that one should first create the appropriate [configs](../general/config.md).
Please see the documentation for wrapped pipelines (`Mapping` and `Flexiprep`) for their configuration options and flags.
Specific configuration values for the Sage pipeline are:
| Name | Type | Function |
| ---- | ---- | -------- |
| countbed | Path (required) | Path to count bed file |
| squishedcountbed | Path (optional) | By supplying this file the auto squish job will be skipped |
| transcriptome | Path (required) | Fasta file for transcriptome. Note: Must come from Ensembl! |
| tags_library | Path (optional) | Five-column tab-delimited file (<tag> <firstTag> <AllTags> <FirstAntiTag> <AllAntiTags>). Unsupported option |
## Running Sage ## Running Sage
As with other pipelines, you can run the Sage pipeline by invoking the `pipeline` subcommand. There is also a general help available which can be invoked using the `-h` flag: As with other pipelines, you can run the Sage pipeline by invoking the `pipeline` subcommand. There is also a general help available which can be invoked using the `-h` flag:
...@@ -27,13 +38,12 @@ As with other pipelines, you can run the Sage pipeline by invoking the `pipeline ...@@ -27,13 +38,12 @@ As with other pipelines, you can run the Sage pipeline by invoking the `pipeline
$ java -jar /path/to/biopet.jar pipeline sage -h $ java -jar /path/to/biopet.jar pipeline sage -h
Arguments for Sage: Arguments for Sage:
-outDir,--output_directory <output_directory> Output directory -s,--sample <sample> Only Sample
--countbed <countbed> countBed -config,--config_file <config_file> JSON / YAML config file(s)
--squishedcountbed <squishedcountbed> squishedCountBed, by suppling this file the auto squish job will be -cv,--config_value <config_value> Config values, value should be formatted like 'key=value' or
skipped 'path:path:key=value'
--transcriptome <transcriptome> Transcriptome, used for generation of tag library -DSC,--disablescatter Disable all scatters
-config,--config_file <config_file> JSON config file(s)
-DSC,--disablescatterdefault Disable all scatters
~~~ ~~~
If you are on SHARK, you can also load the `biopet` module and execute `biopet pipeline` instead: If you are on SHARK, you can also load the `biopet` module and execute `biopet pipeline` instead:
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