X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/88b5b089f38a587292bb68772251b8275c0e27c7..22db612b913e6b4d68b3600c04d06e4898a2f1a9:/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid diff --git a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid index fbe6786b52..9373c9bb24 100644 --- a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid +++ b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid @@ -4,12 +4,26 @@ navsection: userguide title: "Running a pipeline using Workbench" ... -# Go to "Collections":http://{{ site.arvados_workbench_host }}/collections -# Go to the search box and search for "tutorial". -# This should yield a collection with the contents "var-GS000016015-ASM.tsv.bz2" -# Click on the check box to the left of "var-GS000016015-ASM.tsv.bz2". This puts the collection in your persistent selection list. Click on the paperclip in the upper right to see your selections. -# Click on "Pipeline templates":http://{{ site.arvados_workbench_host }}/pipeline_templates -# Look for a pipeline named "Tutorial pipeline" -# Click on the play button on the left. This will take you to the new pipeline page. -# Next to "input" click on "none" to set the input value. At the top of the list will be the collection that you selected in step 4. -# You can now click on "Run pipeline" in the upper right to start the pipeline. +A "pipeline" (sometimes called a "workflow" in other systems) is a sequence of steps that apply various programs or tools to transform input data to output data. Pipelines are the principal means of performing computation with Arvados. This tutorial demonstrates how to run a single-stage pipeline to take a small data set of paired-end reads from a sample "exome":https://en.wikipedia.org/wiki/Exome in "FASTQ":https://en.wikipedia.org/wiki/FASTQ_format format and align them to "Chromosome 19":https://en.wikipedia.org/wiki/Chromosome_19_%28human%29 using the "bwa mem":http://bio-bwa.sourceforge.net/ tool, producing a "Sequence Alignment/Map (SAM)":https://samtools.github.io/ file. This tutorial will introduce the following Arvados features: + +