Conduct a review of existing analysis platform options and summarize in a Supplementary Table

[malachig]

We need summarize competing initiatives to the GMS and provide a reference table describing the current lay of the land with respect to relevant existing resources.

• GATK's Queue (http://gatkforums.broadinstitute.org/discussion/1306/overview-of-queue)
• Arvados
• bcbio-nextgen
• ‘ga4gh’
• gkno. http://gkno.me/
• Illumina base space
• CGA's Firehose (http://www.broadinstitute.org/cancer/cga/Firehose)
• Galaxy (https://usegalaxy.org)
• Seven Bridges Genomics (https://www.sbgenomics.com)
• DNA Nexus Platform (https://www.dnanexus.com)
• Curoverse's Arvados (https://arvados.org)
• Appistry's Ayrris (http://www.appistry.com/products/ayrris)
• IBM's PowerGene Orchestrator (http://tech.journeytofrontier.com/2014/04/how-about-true-workflow-engine.html)
• Taverna
• KNIME
• Bioclipse

For each of these we want to assess the following criteria:

• Published? If so, provide citation
• Source code available? If so provide URL
• Commercial product? Non-commercial? Uncertain?
• Provides complete pipelines for which of the following: germline/reference-alignment?, somatic variation (what kinds)?, rna-seq expression and fusion detection?, differential expression?, clinical interpretation?
• Requirement to install tools as dependencies yourself?
• Ready to use on cloud?
• workflow manager included?
• job scheduler included?
• data and analysis tracking/provenance?

Note that the GMS is much more than just a workflow system. If any of the above are generic workflow management platforms, we can take note of them but they will not be in the final table. The table should only include analysis platforms that have value added for genome analysis specifically.

[malachig]

The next step is make a version of this table (currently in Google doc) that can be embedded in the GMS Wiki. I will attempt this using the Google docs publishing options.

[malachig]

Apparently you can not embed a google doc in a github wiki. For now I have created a page and linked to the URL for the published Google Doc. This is probably fine for now.

[malachig]

A draft of this table is now in place as Supplementary Table 6 of the manuscript.

A more detailed version in Google spreadsheet is available here: https://docs.google.com/spreadsheets/d/1o8iYwYUy0V7IECmu21Und3XALwQihioj23WGv-w0itk/pubhtml

A Wiki page linking to this resource is available here: https://github.com/genome/gms/wiki/The-GMS-compared-to-conceptually-related-resources

We should maintain the online version with updates as the field progresses. Closing this issue for now.