@omicverse/dsh-omicos

Run OmicVerse/OmicOS bioinformatics analyses from inside DeepSeek Harness. The dsh agent keeps the wheel; this plugin gives it a persistent Python kernel (scanpy / omicverse / R) plus the catalog of analysis skills that OmicOS ships.

中文简介：把 OmicOS 的生信分析能力接进 dsh。DeepSeek 负责对话与规划， OmicOS 负责跑分析——持久 Python 内核，adata 等状态跨轮累积； 另带账号/订阅标签页与实时执行过程可视化。

dsh plugin --profile web add @omicverse/dsh-omicos

Tools

One tool runs an analysis; the rest are direct reads of the local kernel that cost neither a turn nor a token.

Tool	What it does
omicos_analyze	Runs a full OmicOS turn in a persistent kernel bound to the workspace. Repeated calls in one dsh session land on the same OmicOS conversation, so state accumulates. background: true hands it to ctx.jobs with live tqdm progress.
omicos_capabilities	Searches the installed skill/agent catalog (several hundred skills and ~100 agents on a full install) and returns a ranked, bounded projection. Use it to decide whether a task is worth delegating. Omit the query for a category overview.
omicos_list_variables	What currently lives in the kernel — name, type, shape, size.
omicos_query_variable	One variable in detail. For an AnnData this includes the preprocessing state (is_int / is_normalized / is_log1p / is_scaled), which is what decides whether the next step is legal.
omicos_list_generated_files	Every file the analyses of this conversation produced.

Commands

/omicos-help (what the plugin adds, and where to look), /omicos-login (device-code pairing — sign in with phone or email in the browser), /omicos-status, /omicos-account, /omicos-logout, /omicos-stop-kernel.

Deliberately short: commands are for what the agent cannot do for you. Listing variables, browsing capabilities or finding outputs is better asked of the agent, which has tools for exactly that.

UI

The client bundle adds two surfaces to the web profile:

• an OmicOS tab next to the conversation — a small console: sign-in state, plan and expiry with links to subscribe or manage; which kernels are attached, where, at what version, and what is bound in them right now; and a search box over the installed capability catalog;
• a live tool view on omicos_analyze calls — the steps, tool calls and stdout tail as the analysis runs, instead of a spinner that ends in a wall of text. Generated figures render in the settled card.

If dsh-better-sidebar is installed, an "OmicOS 产物" tab is registered there too; the integration is optional and detected at runtime.

Requirements

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