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Bpipe

Comparison To Workflow Tools. Using the bpipe command. Example With Inputs And Outputs. Implementing A Resource Manager. Listening for Pipeline Events. Bpipe provides a platform for running big bioinformatics jobs that consist of a series of processing stages - known as 'pipelines'. July 18th, 2016 - New! Bpipe 0.9.9.2 released! Bpipe has been published in Bioinformatics. If you use Bpipe, please cite:. By turning your shell scripts into Bpipe scripts, here are some of the features you can get:. Bpipe ma...

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Comparison To Workflow Tools. Using the bpipe command. Example With Inputs And Outputs. Implementing A Resource Manager. Listening for Pipeline Events. Bpipe provides a platform for running big bioinformatics jobs that consist of a series of processing stages - known as 'pipelines'. July 18th, 2016 - New! Bpipe 0.9.9.2 released! Bpipe has been published in Bioinformatics. If you use Bpipe, please cite:. By turning your shell scripts into Bpipe scripts, here are some of the features you can get:. Bpipe ma...

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Bpipe | docs.bpipe.org Reviews

https://docs.bpipe.org

Comparison To Workflow Tools. Using the bpipe command. Example With Inputs And Outputs. Implementing A Resource Manager. Listening for Pipeline Events. Bpipe provides a platform for running big bioinformatics jobs that consist of a series of processing stages - known as 'pipelines'. July 18th, 2016 - New! Bpipe 0.9.9.2 released! Bpipe has been published in Bioinformatics. If you use Bpipe, please cite:. By turning your shell scripts into Bpipe scripts, here are some of the features you can get:. Bpipe ma...

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docs.bpipe.org

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Extension Syntax - Bpipe

http://docs.bpipe.org/Language/ExtensionSyntax

Comparison To Workflow Tools. Using the bpipe command. Example With Inputs And Outputs. Implementing A Resource Manager. Listening for Pipeline Events. Extension syntax for referencing input and output variables. Extension syntax for referencing input and output variables. Will refer to the. Output from the previous pipeline stage - but what if that stage has multiple outputs and it changes their order? Align reads = { exec bowtie S reference $input.fastq samtools view -bSu - $output.bam }. Statement to ...

2

Comparison To Workflow Tools - Bpipe

http://docs.bpipe.org/Overview/ComparisonToWorkflowTools

Comparison To Workflow Tools. Using the bpipe command. Example With Inputs And Outputs. Implementing A Resource Manager. Listening for Pipeline Events. How Bpipe Compares to other Tools. What about a GUI? How Bpipe Compares to other Tools. Built in Cluster Support. Online Data Source Integration. Easy Shell Script Portability. What about a GUI? Documentation built with MkDocs.

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Check - Bpipe

http://docs.bpipe.org/Language/Check

Comparison To Workflow Tools. Using the bpipe command. Example With Inputs And Outputs. Implementing A Resource Manager. Listening for Pipeline Events. Check { statements to validate results } otherwise { statements to execute on failure } check( check name ) { statements to validate results } otherwise { statements to execute on failure }. Statement gives a convenient way to implement validation of a pipeline's outputs or progress and implement an alternative action if the validation fails. The. Due to ...

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Parallel Tasks - Bpipe

http://docs.bpipe.org/Language/ParallelTasks

Comparison To Workflow Tools. Using the bpipe command. Example With Inputs And Outputs. Implementing A Resource Manager. Listening for Pipeline Events. Running Pipeline Stages in Parallel. Executing Multiple Stages Simultaneously on the Same Data. Parallelizing Based on Chromosome. Executing Multiple Stages Simultaneously on Different Data. Running Pipeline Stages in Parallel. You have one set of data (eg. a sample) that needs to undergo several independent operations that can be done at the same time.

5

Grep - Bpipe

http://docs.bpipe.org/Language/Grep

Comparison To Workflow Tools. Using the bpipe command. Example With Inputs And Outputs. Implementing A Resource Manager. Listening for Pipeline Events. Grep( regular expression ) { statements that execute for each line matching expression }. Grep( regular expression ). Statement is an internal convenience function that processes the input file line by line for each line matching a given regular expression. Is defined. The body can execute regular commands using exec. In the second form.

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GitHub - ssadedin/bpipe: Bpipe - a tool for running and managing bioinformatics pipelines

https://github.com/ssadedin/bpipe

Bpipe - a tool for running and managing bioinformatics pipelines. Http:/ docs.bpipe.org/. Use Git or checkout with SVN using the web URL. Aug 8, 2016. Add some quick docs about pipeline events. Failed to load latest commit information. Fix torque custom options separated from pbs directives. Aug 8, 2016. Add some quick docs about pipeline events. Aug 9, 2016. Added example for how to run paired end reads. Feb 21, 2013. Update gradle wrapper to 2.0 (support for JDK9). Aug 23, 2015. May 31, 2016. Sadedin S...

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docs.bpipe.org

Bpipe

Comparison To Workflow Tools. Using the bpipe command. Example With Inputs And Outputs. Implementing A Resource Manager. Listening for Pipeline Events. Bpipe provides a platform for running big bioinformatics jobs that consist of a series of processing stages - known as 'pipelines'. July 18th, 2016 - New! Bpipe 0.9.9.2 released! Bpipe has been published in Bioinformatics. If you use Bpipe, please cite:. By turning your shell scripts into Bpipe scripts, here are some of the features you can get:. Bpipe ma...

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