Arvados enables you to quickly begin using cloud computing resources in your data science work. It allows you to track your methods and datasets, share them securely, and easily re-run analyses.

Check out our developer site. We're open source, check out our code on github. diff --git a/doc/user/getting_started/community.html.textile.liquid b/doc/user/getting_started/community.html.textile.liquid index 8b6e22d1fd..7ef903c3de 100644 --- a/doc/user/getting_started/community.html.textile.liquid +++ b/doc/user/getting_started/community.html.textile.liquid @@ -6,7 +6,7 @@ title: Arvados Community and Getting Help h2. On the web -The Arvados Free Sofware project page is located at "http://arvados.org":http://arvados.org . The "Arvados Wiki":https://arvados.org/projects/arvados/wiki is a collaborative site for documenting Arvados has an overview of the Arvados Platform and Components. The "Arvados blog":https://arvados.org/projects/arvados/blogs posts articles of interest about Arvados. +The Arvados Free Sofware project page is located at "http://arvados.org":http://arvados.org . The "Arvados Wiki":https://arvados.org/projects/arvados/wiki is a collaborative site for documenting Arvados and provides an overview of the Arvados Platform and Components. The "Arvados blog":https://arvados.org/projects/arvados/blogs posts articles of interest about Arvados. h2. Mailing lists @@ -14,7 +14,7 @@ The "Arvados user mailing list":http://lists.arvados.org/mailman/listinfo/arvado h2. IRC -The "#arvados":irc://irc.oftc.net:6667/#arvados IRC (Internet Relay Chat) channel at on the "Open and Free Technology Community (irc.oftc.net)":http://www.oftc.net/oftc/ is available for live discussion and support. You can use a traditional IRC client or "join OFTC over the web.":https://webchat.oftc.net/?channels=arvados +The "#arvados":irc://irc.oftc.net:6667/#arvados IRC (Internet Relay Chat) channel at the "Open and Free Technology Community (irc.oftc.net)":http://www.oftc.net/oftc/ is available for live discussion and support. You can use a traditional IRC client or "join OFTC over the web.":https://webchat.oftc.net/?channels=arvados h2. Bug tracking diff --git a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid index 8dad6ab25e..f9522fbef0 100644 --- a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid +++ b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid @@ -6,7 +6,7 @@ title: "Running a pipeline using Workbench" 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: -

* How to create a new pipeline from an existing template. * How to browse and select input data for the pipeline and submit the pipeline to run on the Arvados cluster. * How to access your pipeline results. @@ -14,13 +14,15 @@ A "pipeline" (sometimes called a "workflow" in other systems) is a sequence of s notextile.

+h3. Steps + # Start from the *Workbench Dashboard*. You can access the Dashboard by clicking on * Dashboard* in the upper left corner of any Workbench page. # Click on the Run a pipeline... button. This will open a dialog box titled *Choose a pipeline to run*. # Click to open the *All projects * menu. Under the *Projects shared with me* header, select * Arvados Tutorial*. # Select * Tutorial align using bwa mem* and click the Next: choose inputs button. This will create a new pipeline in your *Home* project and will open it. You can now supply the inputs for the pipeline. -# The first input parameter to the pipeline is *Reference genoma (fasta)*. Click the Choose button beneath that header. This will open a dialog box titled *Choose a dataset for Reference genome (fasta)*. +# The first input parameter to the pipeline is *"reference_collection" parameter for run-command script in bwa-mem component*. Click the Choose button beneath that header. This will open a dialog box titled *Choose a dataset for "reference_collection" parameter for run-command script in bwa-mem component*. # Once again, open the *All projects * menu and select * Arvados Tutorial*. Select * Tutorial chromosome 19 reference* and click the OK button. -# Repeat the previous two steps to set the *Input genome (fastq)* parameter to * Tutorial sample exome*. +# Repeat the previous two steps to set the *"sample" parameter for run-command script in bwa-mem component* parameter to * Tutorial sample exome*. # Click on the Run button. The page updates to show you that the pipeline has been submitted to run on the Arvados cluster. # After the pipeline starts running, you can track the progress by watching log messages from jobs. This page refreshes automatically. You will see a complete label under the *job* column when the pipeline completes successfully. # Click on the *Output* link to see the results of the job. This will load a new page listing the output files from this pipeline. You'll see the output SAM file from the alignment tool under the *Files* tab.