Parse sequences in Rust/wasm #4
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I updated A LOT of dependencies, please let me know if I overdid it 😅 |
luizirber
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I added the |
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@luizirber Thank you very much for this PR! @MGS-sails : let's have a chat about this one, I think you were interested in looking into this web assembly piece? |
@SandyRogers Yes, It'd be great to have a chat about this. Thanks !! |
luizirber
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Now it uses the released sourmash 0.13.1 |
Co-authored-by: Tessa Pierce Ward <bluegenes@users.noreply.github.com>
- Allow running in {docker,podman}-compose
- Add docs and initial tutorial for deploying a new instance with
example datasets
- Bring in the search index as additional Docker container in compose
- Use pixi for dep management
- Trigger metadata update for mongodb outside image creation, use only
one mongodb container in compose
- Add sentry for monitoring (opt-in)
- Flask app checks for errors from the search index
- Use docker links to connect to mongodb and search index by container
name
- Update mgnify component to (unreleased) one containing better sequence
parsing:
EBI-Metagenomics/mgnify-sourmash-component#4
- Update sourmash to 0.13.0 (rust) and use new APIs for revindex
- Add snakemake rules for building search index from example datasets
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Co-authored-by: Tessa Pierce Ward <bluegenes@users.noreply.github.com>
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@luizirber sorry for taking so long to get back to you on this. |
sourmash-bio/sourmash#3047 implemented sequence parsing using
niffler+needletail, which allows FASTA/FASTQ, as well asgzor uncompressed files.This PR are the changes needed to use the package generated from that PR. Once that PR is merged and released it can be used directly here, but wanted to leave this open to allow commenting on the changes I did to make it work on the component.