bilayer-containers
Projects to put ourselves in the context of #67
Replies: 11 comments 1 reply
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Album - Preprint includes Kyle Harrington, now of Napari (and frequent Eliceiri lab collab if I understand correctly). For imaging tools, which is neat! Love the idea of the catalog of tools/steps being federated. |
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EU Workflow Hub - Repository of workflows. Lists about 30 kinds of workflows you can deposit (and counting) |
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Common Workflow Language - this was the thing I was most frequently asked how we intersect with. Certainly worth a discussion, before it's too late to pivot, if we should think about extending their tool specification rather than our own |
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Workflow Description Language - it's made at Broad and is what Terra uses. Probably need a deeper dive on this sometime. |
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Dockstore - "An App Store for Bioinformatics". Describes tools and supports description in "Common Workflow Language (CWL), Workflow Description Language (WDL), Nextflow (NFL), and Galaxy". |
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biop-desktop website / github of base image - one (ish) tool at a time, container launches a whole desktop (but seemingly differently than the one time Callum played with this, which was using xpra, they're using TigerVNC and noVNC. Talked a bit about it with Romain at I2K but he said he was not the right person for deep tech stack questions (but could connect us to who was). |
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Nextflow |
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Snakemake |
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Galaxy |
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"There are 362 standards" |
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Bio.tools, a tool collection website |
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We're not the only people out there building stuff! Which is not to say multiple solutions to the same problem aren't sometimes needed, but tracking similar-ish projects (ideally who we can learn from and/or collaborate).
At least some of these are workflow runners, which we adamantly are not (and do not want to be), but in being workflow runners, they usually have some sort of a "tool description spec"
(When we go to write the preprint, eventually, future-us's will hopefully also be grateful)
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