From f9c6685c494d6bb63526774a99b3af411386f071 Mon Sep 17 00:00:00 2001 From: Manish Kumar Date: Fri, 7 Aug 2026 22:21:49 -0500 Subject: [PATCH] docs: fix stale org/repo links, correct plugin count - ghcr.io/man4ish/omnibioai-dev-env (badge, docker pull/build) and the clone command's github.com/man4ish/omnibioai-dev-docker -> OmniBioAI org, same pattern fixed in ten other repos today. - The "Part of the OmniBioAI Ecosystem" link pointed at github.com/man4ish/omnibioai -- wrong org and wrong repo name (the real repo is OmniBioAI/omnibioai-workbench; the local omnibioai/ checkout directory name differs from its GitHub name, confirmed via git remote -v there earlier this session). Fixed, and corrected "200+ bioinformatics plugins" to the verified 231 enabled (that repo's own README was corrected to this figure earlier today). Co-Authored-By: Claude Sonnet 5 --- README.md | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 81a345d..d1b18d3 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ > Full AI/Bioinformatics development environment for GPU/DGX machines. > Built on NVIDIA PyTorch 25.10 with CUDA support. -[![Docker](https://img.shields.io/badge/ghcr.io-omnibioai--dev--env-blue?logo=docker)](https://ghcr.io/man4ish/omnibioai-dev-env) +[![Docker](https://img.shields.io/badge/ghcr.io-omnibioai--dev--env-blue?logo=docker)](https://ghcr.io/omnibioai/omnibioai-dev-env) [![License](https://img.shields.io/badge/license-Apache%202.0-green)](LICENSE) [![GPU Required](https://img.shields.io/badge/GPU-required-orange?logo=nvidia)](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html) @@ -65,15 +65,15 @@ This is **not** part of the OmniBioAI production stack. It is not: ### Option A — Pull from GHCR (recommended) ```bash -docker pull ghcr.io/man4ish/omnibioai-dev-env:latest +docker pull ghcr.io/omnibioai/omnibioai-dev-env:latest bash run_ai_dev.sh ``` ### Option B — Build locally ```bash -git clone https://github.com/man4ish/omnibioai-dev-docker +git clone https://github.com/OmniBioAI/omnibioai-dev-docker cd omnibioai-dev-docker -docker build -t ghcr.io/man4ish/omnibioai-dev-env:latest . +docker build -t ghcr.io/omnibioai/omnibioai-dev-env:latest . bash run_ai_dev.sh ``` @@ -209,10 +209,11 @@ sc.pl.pca_variance_ratio(adata) ## Part of the OmniBioAI Ecosystem This dev environment is designed to work alongside the -[OmniBioAI platform](https://github.com/man4ish/omnibioai) — +[OmniBioAI platform](https://github.com/OmniBioAI/omnibioai-workbench) +(checked out locally as `omnibioai/`) — a unified AI-powered bioinformatics workbench supporting: -- 200+ bioinformatics plugins +- 231 enabled bioinformatics plugins - RNA-seq, single-cell, spatial omics, variant calling - TES workflow execution (Slurm, K8s, AWS Batch, Azure) - RAG-powered literature search (PubMed + FAISS) @@ -234,5 +235,5 @@ If you use this environment in your research, please cite: ``` OmniBioAI Dev Environment (2025) Manish Kumar -https://github.com/man4ish/omnibioai-dev-docker +https://github.com/OmniBioAI/omnibioai-dev-docker ```