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jplfariaclaude
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Add Open PRs + Pending Handoffs tracking section
Surfaces what is blocked on whom (importer PR for mmseqs2 review, CTS admin registration for kofamscan and bakta) so we don't lose track of in-flight work. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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README.md

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| Tool | Repo | Image | Refdata | Status |
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|------|------|-------|---------|--------|
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| mmseqs2 | [cdm_mmseqs2](https://github.com/kbaseincubator/cdm_mmseqs2) | `0.1.0` | no | Live (importer PR #35 pending merge in cdm-spark-events-importers) |
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| mmseqs2 | [cdm_mmseqs2](https://github.com/kbaseincubator/cdm_mmseqs2) | `0.1.0` | no | Live, importer pending merge ([PR #35](https://github.com/kbase/cdm-spark-events-importers/pull/35)) |
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| kofamscan | [cdm_kofamscan](https://github.com/kbaseincubator/cdm_kofamscan) | `0.1.0` | KEGG HMMs (~1.5GB bundled, staged at `cts/io/jplfaria/refdata_staging/kofam/`) | Awaiting registration |
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| bakta | [cdm_bakta](https://github.com/kbaseincubator/cdm_bakta) | `0.1.0` | Bakta DB v6 full (~30GB bundled, staged at `cts/io/jplfaria/refdata_staging/bakta/`) | Awaiting registration |
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| gtdbtk ||| ~100GB taxonomy DB | Planned |
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| eggNOG ||| eggNOG DB | Planned |
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| RAST ||| none | Planned (custom container talk to Bill) |
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| RAST ||| none | Planned (custom container, talk to Bill) |
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| psortb ||| none | Planned |
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| transyt ||| none | Planned (custom container) |
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| modelseedpy ||| none | Planned (ask Chris Henry for container) |
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External / not built via this skeleton:
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- **checkm2**`ghcr.io/kbasetest/cdm_checkm2:0.3.0` (Gavin's reference example, predates this skeleton)
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- **InterProScan** — Chris Neely's container (deployed to dev only, currently broken)
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---
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## Open PRs and Pending Handoffs
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Things waiting on someone else. Update as items move.
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### Open PRs
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| PR | Tool | Description | Owner / waiting on |
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|----|------|-------------|-------------------|
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| [kbase/cdm-spark-events-importers#35](https://github.com/kbase/cdm-spark-events-importers/pull/35) | mmseqs2 | First importer for the cluster TSV output. CI green, ready to merge. | Gavin (review + merge + redeploy event processor) |
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### Pending CTS admin (Gavin) registrations
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| Tool | What's needed | Staged at |
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|------|---------------|-----------|
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| kofamscan | Move bundle to `cts-refdata`, register refdata, register image with refdata link | `s3://cts/io/jplfaria/refdata_staging/kofam/kofam_refdata.tar.gz` (~1.5GB), image `ghcr.io/kbaseincubator/cdm_kofamscan:0.1.0@sha256:d6b20eccf4c6bf1b095e530844a8b04dbae5fca85daf0c9b2bdffb0cf10a9a42` |
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| bakta | Move bundle to `cts-refdata`, register refdata, register image with refdata link | `s3://cts/io/jplfaria/refdata_staging/bakta/bakta_db.tar.gz` (~30GB), image `ghcr.io/kbaseincubator/cdm_bakta:0.1.0@sha256:6de4c51cadd75bc6a1d9f6e6b05716ecfdcfa63510b82459477ff757200d8d06` |

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