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- GenoBank.io BioNFT-Gated Filesystem CLI with Sequentia Protocol (BioCIDRegistry, ConsentManager, BioPIL) - 97% cost savings vs Story Protocol","maintainers":[{"name":"genobank","email":"daniel@genobank.io"}],"readme":"# BioFS — GenoBank.io CLI\n\n> **BioNFT-gated genomic data, meet standard bioinformatics tools.**\n> Stream, view, mount, and analyze consent-gated VCFs / BAMs / FASTQs with\n> `bcftools`, `samtools`, `pysam`, `IGV`, and every tool you already use —\n> no FUSE install, no kext, no data copy.\n\n[![npm version](https://img.shields.io/npm/v/@genobank/biofs.svg)](https://www.npmjs.com/package/@genobank/biofs)\n[![License: AGPL-3.0](https://img.shields.io/badge/License-AGPL_3.0-blue.svg)](LICENSE)\n\n---\n\n## What you can do in 30 seconds\n\n```bash\nnpm install -g @genobank/biofs      # once\nbiofs login                          # browser pops up, sign with your wallet\nbiofs files                          # see what's accessible to you\nbiofs stream <ip_id> | bcftools stats -    # live-analyze a VCF you own\n```\n\nThat's it. BioNFT ownership is verified on every request; revocation is immediate;\nnothing ever hits your disk unless you ask for it.\n\n---\n\n## Table of contents\n\n- [Install](#install)\n- [Authentication](#authentication)\n- [Discover your BioIPs](#discover-your-bioips)\n- [Streaming & analysis — NEW in v2.7](#streaming--analysis--new-in-v27)\n- [Downloads](#downloads)\n- [Mounting as a filesystem](#mounting-as-a-filesystem)\n- [Uploading & tokenization](#uploading--tokenization)\n- [Access control & sharing](#access-control--sharing)\n- [Running research jobs (BioOS)](#running-research-jobs-bioos)\n- [BioContext manifests](#biocontext-manifests)\n- [Aliases — never type hex again](#aliases--never-type-hex-again)\n- [BioCID format](#biocid-format)\n- [Configuration](#configuration)\n- [Troubleshooting](#troubleshooting)\n- [Security model](#security-model)\n- [Development](#development)\n- [License](#license)\n\n---\n\n## Install\n\n**Requires:** Node.js 18+ (uses built-in `fetch`).\n\n```bash\n# Globally (recommended)\nnpm install -g @genobank/biofs\n\n# Verify\nbiofs --version        # → 2.7.1\n```\n\nOptional but highly recommended for researchers:\n\n```bash\n# macOS\nbrew install bcftools samtools htslib\n\n# Debian / Ubuntu\nsudo apt-get install bcftools samtools tabix\n```\n\nThe CLI works without these; they unlock `biofs pipe` and `biofs view`\nfilesystem-level integration.\n\n---\n\n## Authentication\n\n```bash\nbiofs login\n# Browser opens → MetaMask / Magic Link → sign \"I want to proceed\"\n# ✅ Authenticated as: 0x5f5a60…Ed19a\n```\n\nCredentials live at `~/.biofs/credentials.json` (0600, owner-only). The\nsignature is an EIP-191 `personal_sign` of the string `\"I want to proceed\"`\n— re-usable by the CLI for the next ~30 days before you need to re-sign.\n\n```bash\nbiofs whoami     # show current wallet\nbiofs logout     # clear cached credentials (securely overwrites then deletes)\n```\n\n---\n\n## Discover your BioIPs\n\n```bash\nbiofs files                      # full table of everything you can access\nbiofs files --filter vcf         # only VCFs\nbiofs files --source story       # only Story Protocol IP Assets\nbiofs files --source avalanche   # only Avalanche-side biosamples\n```\n\nEach row shows the BioCID, ip_id, filename, owner, license status, and\nstorage backend (S3 / GCS / Story / Avalanche).\n\n---\n\n## Streaming & analysis — NEW in v2.7\n\nThis is what most Mac / Linux researchers will use daily. Zero setup;\npipes cleanly into the tools you already have.\n\n### `biofs stream` — raw bytes to stdout\n\n```bash\nbiofs stream 0xCCe14315eE3D6a41596EeB4a2839eE50A8ec59f7 | bcftools stats -\nbiofs stream my-wes | bcftools view -H - | head\nbiofs stream my-bam | samtools view -c -     # count reads\nbiofs stream my-wes | python - <<'PY'\nimport pysam, sys\nfor v in pysam.VariantFile(sys.stdin):\n    print(v.chrom, v.pos, v.ref, v.alts)\nPY\n```\n\nFlags:\n- `--kind variants|reads` force the htsget datatype (default: auto-detect from filename)\n- `--htsget-url <url>` override the endpoint (default: `https://htsget.genobank.app`)\n\n### `biofs pipe` — auto-pipe into the right tool\n\nDetects the file format from the registered filename and pipes the\nstream straight into `bcftools view` (VCF) or `samtools view` (BAM).\nEverything after `--` is passed through to the tool.\n\n```bash\nbiofs pipe my-wes -- -H                       # bcftools view -H\nbiofs pipe my-wes -- -r chr17                 # region filter (client-side)\nbiofs pipe my-wes -- -s SAMPLE01              # single sample\nbiofs pipe my-bam -- -b | samtools sort       # chain\n```\n\n### `biofs view` — print file content (not piped to a tool)\n\nFor small files (DTC TXT, CSV, JSON, metadata). Respects GDPR \"Right to\nAccess\" audit logging server-side.\n\n```bash\nbiofs view my-dtc --lines 50\nbiofs view my-report.json --format pretty\n```\n\n### `biofs htsget` — low-level GA4GH htsget (debugging)\n\n```bash\nbiofs htsget service-info\nbiofs htsget ticket variants my-wes          # raw ticket JSON\nbiofs htsget ticket reads my-bam\n```\n\nEndpoint: `https://htsget.genobank.app` (GA4GH v1.2 compliant).\nAuth: `Authorization: Bearer <signature>` (same signature as `biofs login`).\n\n---\n\n## Downloads\n\nWhen you want the file on disk (not streaming):\n\n```bash\nbiofs download my-wes                              # to ./55052008714000.deepvariant.vcf\nbiofs download my-wes ~/analysis/                  # into a directory\nbiofs download my-wes /tmp/sample.vcf              # exact path\nbiofs download --force my-wes                      # overwrite existing\n```\n\nDownloads verify BioNFT ownership on every request and log access for\nGDPR Article 15 (Right to Access). Large files show a progress bar; use\n`--quiet` / `-q` to silence.\n\nGDPR-compliant variant (explicit consent prompt):\n\n```bash\nbiofs download-with-consent my-wes\n```\n\n---\n\n## Mounting as a filesystem\n\nThree methods, pick based on your platform and use case:\n\n| Method | When to use | Requires |\n|---|---|---|\n| `copy`  | Simple local work on a small set of files | nothing |\n| `nfs`   | Full filesystem semantics on Linux / macOS | BioNFS server + NFS client |\n| `fuse`  | **Recommended** for native Unix tool access | `biofs-fuse` binary + FUSE / macFUSE |\n\n```bash\n# 1. Copy method — downloads files on demand, read/write\nbiofs mount /mnt/bio --method copy\n\n# 2. NFS method — live mount via bionfs server\nbiofs mount /mnt/bio --method nfs --biocid biocid://v1/sequentia/IPA/0x…/0x…\n\n# 3. FUSE method — Rust-backed driver, lowest latency, xattrs exposed\nbiofs mount /mnt/bio --method fuse --biocid biocid://v1/sequentia/IPA/0x…/0x…\n\n# Once mounted, use any Unix tool\nls -la /mnt/bio/\nbcftools view /mnt/bio/sample.vcf | head\nigv /mnt/bio/sample.vcf\ncat /mnt/bio/.status                   # FUSE-only: consent + owner info\n\n# Unmount\nbiofs umount /mnt/bio\n```\n\n**FUSE installation:**\n\n- **macOS:** `brew install --cask macfuse` (first time needs kext approval + restart) **or** `brew install --cask fuse-t` (no reboot)\n- **Linux:** `sudo apt install fuse3 libfuse3-dev`\n- **biofs-fuse binary:** `git clone github.com/Genobank/biofs-fuse && cd biofs-fuse && cargo build --release`\n\nSee [biofs-fuse README](https://github.com/Genobank/biofs-fuse) for full setup.\n\n**Remote mount on a GPU agent** (for running pipelines on a separate machine):\n\n```bash\nbiofs mount-remote <biosample_id> --agent <agent_wallet>\n```\n\n---\n\n## Uploading & tokenization\n\nSimple upload:\n\n```bash\nbiofs upload ~/data/sample.vcf                          # to your BioFS S3\nbiofs upload ~/data/reads.fastq.gz --type fastq         # force file type\n```\n\nUpload + tokenize as BioNFT:\n\n```bash\nbiofs tokenize file ~/data/sample.vcf                   # VCF → BioIP NFT\nbiofs tokenize biosample <biosample_serial>             # whole biosample\nbiofs tokenize fastqs <biosample_serial>                # just the FASTQs\n```\n\nOptions:\n- `--title \"...\"` custom NFT title (default: AI-generated from content)\n- `--description \"...\"` custom description\n- `--license {commercial,non-commercial,exclusive,public-good,gdpr-research,ai-training,clinical-use,pharma-research,family-inheritance}` — see [Dual PIL architecture](#dual-pil-architecture) below\n- `--no-ai` skip AI classification\n- `--quiet` no interactive prompts (for scripting)\n\n**Dual PIL architecture** (license values for `--license`):\n- **Story Protocol PIL** (permanent, `non-commercial`, `commercial`, `exclusive`, `public-good`)\n- **Sequentia BioPIL** (revocable, GDPR-compliant, `gdpr-research`, `ai-training`, `clinical-use`, `pharma-research`, `family-inheritance`)\n\n---\n\n## Access control & sharing\n\n```bash\n# Request access to someone else's BioIP\nbiofs access request <ip_id> --message \"needed for chr17 study\"\n\n# Grant access (as the owner, to a requester)\nbiofs access grant <request_id> <receiver_wallet>\n\n# Revoke access you previously granted\nbiofs access revoke <request_id>\n\n# Revoke your own biosample consent (GDPR Article 17 — Right to Erasure)\n# Note: triggers off-chain S3 deletion via the BioRouter event listener.\nbiofs access revoke-consent <biocid>\n\n# See who has access to what\nbiofs access list                   # access you've granted\nbiofs shares                        # full permission graph (by you + to you)\n\n# Ad-hoc share\nbiofs share <biocid_or_filename> --to <receiver_wallet> --license <license_type>\n\n# Check a specific wallet's access to a BioCID\nbiofs access check <biocid> --wallet 0x…\n```\n\n---\n\n## Running research jobs (BioOS)\n\nNatural-language research workflows against your BioIPs:\n\n```bash\nbiofs job pipelines                                    # list available pipelines\nbiofs job create \"Annotate VCF with rare coding variants\" sample.vcf \\\n    --pipeline vcf_annotation\nbiofs job status <job_id> --watch                      # live progress\nbiofs job results <job_id>                             # download result URLs\nbiofs job list --status running                        # your job queue\n```\n\nRun results are themselves tokenizable as derivative BioNFTs — the\nClaraJobNFT contract links each job output back to the source BioIP so\nyou get auditable lineage.\n\nQuick annotation wrapper:\n\n```bash\nbiofs annotate my-wes                                  # OpenCRAVAT with default annotators\nbiofs annotate my-wes --annotators clinvar,cosmic      # pick specific ones\n```\n\n**Agent health** — check if your GPU compute agent is ready:\n\n```bash\nbiofs agent-health\n```\n\n---\n\n## BioContext manifests\n\nEIP-712-signed `.bionft` manifests let you bundle multiple BioIPs into\na single signed context for research group sharing, clinical trials,\nor consortium data-use agreements.\n\n```bash\nbiofs context create --out consortium.bionft \\\n    --include <biocid1> --include <biocid2>\n\nbiofs context publish consortium.bionft                # pin to IPFS + Sequentia\nbiofs context verify consortium.bionft                 # check signatures + revocations\nbiofs context revoke consortium.bionft                 # propagate revocation\n```\n\n---\n\n## Aliases — never type hex again\n\nLocal shortcuts stored at `~/.biofs/aliases.json`:\n\n```bash\nbiofs alias my-wes 0xCCe14315eE3D6a41596EeB4a2839eE50A8ec59f7\nbiofs alias my-bam 0x9a3E6aEb78363C0b8E240Cc19803d9fe626381C4\nbiofs alias --list\n\nbiofs stream my-wes | bcftools stats -                 # works everywhere\nbiofs pipe   my-wes -- -r chr17\nbiofs view   my-wes\nbiofs download my-wes /tmp/\n\nbiofs alias --remove my-wes\n```\n\nAliases only resolve on non-hex, non-BioCID inputs — real `ip_id` values\n(`0x…`) and `biocid://` URLs always pass through untouched, so aliases\ncan never shadow real identifiers.\n\n---\n\n## BioCID format\n\nBioCID is the universal genomic-file identifier used across GenoBank:\n\n```\nbiocid://v1/<chain>/IPA/<collection_address>/<token_id>[/<filename>]\n```\n\nExamples:\n\n```\nbiocid://v1/sequentia/IPA/0x29853ed299B8FBBe16568840F3Bb2A8E40dc7401/0xCCe14315…\nbiocid://v1/story/IPA/0x29853ed299B8FBBe16568840F3Bb2A8E40dc7401/42/sample.bam\nbiocid://v1/aeneid/IPA/0x…/99/reads.fastq.gz\n```\n\n- **`<chain>`** — `sequentia` (primary, GDPR-revocable) or `story` / `aeneid` (Story Protocol mainnet / testnet)\n- **`IPA`** — literal, marks this as an Intellectual-Property-Asset reference\n- **`<collection_address>`** — the SPG/ERC-721 collection contract\n- **`<token_id>`** — the NFT token id (matches the `ip_id` for on-chain lookups)\n- **`<filename>`** — optional; disambiguates multi-file BioNFTs\n\nEvery `biofs` command accepts an `ip_id` (`0x…`), a full BioCID URL,\nor a local alias.\n\n---\n\n## Configuration\n\nFiles under `~/.biofs/`:\n\n| Path | Contents | Mode |\n|---|---|---|\n| `credentials.json` | Signed auth token | `0600` (owner-only) |\n| `aliases.json` | Your local ip_id shortcuts | `0644` |\n| `config.json` | User preferences | `0644` |\n| `cache/` | Per-request metadata cache | |\n| `logs/` | Operation logs | |\n\n### Environment variables\n\n| Var | Default | Purpose |\n|---|---|---|\n| `BIOFS_HTSGET_URL` | `https://htsget.genobank.app` | Override htsget endpoint |\n| `BIOFS_API_URL` | `https://bioip.genobank.app` | Override BioIP API endpoint |\n| `BIOFS_SIGNATURE` | (from `credentials.json`) | Supply signature directly (CI/Docker) |\n| `BIOFS_ALIASES` | `~/.biofs/aliases.json` | Override aliases file path |\n| `DEBUG` | — | `DEBUG=1` enables verbose logging |\n| `NO_COLOR` | — | `NO_COLOR=1` disables ANSI colors |\n\n---\n\n## Troubleshooting\n\n### `ENOENT: no such file or directory, open '~/.biofs/credentials.json'`\n\nYou're not logged in. Run `biofs login`.\n\n### `Signature rejected` / `Expected 65 bytes, got 4`\n\nYour cached signature expired. `biofs logout && biofs login`.\n\n### `htsget NotFound: no BioIP with id …`\n\nThe ip_id doesn't match anything your wallet can access. Check:\n\n```bash\nbiofs files | grep <first 10 chars of ip_id>\nbiofs access list                    # requests pending approval?\n```\n\n### `htsget 401 Unauthorized` / `403 Forbidden`\n\nConsent for that BioIP has been revoked, or your access license expired.\nCheck with the owner or run `biofs access request <ip_id>` again.\n\n### `bcftools: htsget:// Protocol not supported`\n\nHomebrew's default `htslib` ships without htsget compiled in. **Use\n`biofs stream … | bcftools …` instead** — same effect, the CLI does the\nticket dance for you and pipes raw bytes in.\n\n### Mount fails: `mount_macfuse: the file system is not available`\n\nmacFUSE kernel extension not loaded. Either:\n- **One-time approval + reboot:** `sudo kmutil load -p /Library/Filesystems/macfuse.fs/Contents/Extensions/14/macfuse.kext`, then System Settings → Privacy & Security → \"Allow Benjamin Fleischer\" → restart.\n- **No reboot (recommended):** `brew install --cask fuse-t` — drop-in replacement.\n\n### Cloudflare `error code: 1010` on direct `curl`\n\nCloudflare blocks unknown User-Agents. The CLI sends `biofs/2.7.x\n(+https://genobank.io)` automatically. If you're rolling your own script,\nset a real User-Agent:\n\n```bash\ncurl -A 'mytool/1.0' -H \"Authorization: Bearer $SIG\" https://htsget.genobank.app/…\n```\n\n### `biofs` runs but shows an older version\n\nGlobal installs can shadow each other. Check:\n\n```bash\nwhich -a biofs                      # all matches on PATH\nbiofs --version                     # what's actually running\nnpm uninstall -g @genobank/biofs    # remove\nnpm install -g @genobank/biofs@latest\n```\n\n### Get a full diagnostic report\n\n```bash\nbiofs report > biofs-diagnostic.txt\n```\n\nSends nothing over the network. Includes Node version, install path, auth\nstatus, endpoint reachability, mount tool availability, and version drift\ninfo. Attach to any support email.\n\n---\n\n## Security model\n\n- **Authentication**: EIP-191 `personal_sign` of `\"I want to proceed\"`. No passwords, no private keys ever leave your device.\n- **Credentials on disk**: `~/.biofs/credentials.json` is `0600` (owner read/write only). Signatures are never logged or displayed.\n- **Re-verification**: every `stream`, `pipe`, `download`, `mount`, `view` request is gated by a fresh Bearer-auth check against the BioNFT registry on every call — revocation takes effect immediately.\n- **Bearer token in URL?** Only when unavoidable (e.g., signed S3/GCS presigned URLs). Those URLs expire in 1 hour.\n- **Cloudflare TLS** terminates at the edge using the `*.genobank.app` wildcard cert (Google Trust Services).\n- **GDPR**: Sequentia BioPIL supports Article 17 (Right to Erasure) via `biofs access revoke-consent` — triggers server-side S3 deletion. Story Protocol PIL licenses are **permanent** by design; don't use them for personally-identifiable data.\n- **Auto-expiry**: cached credentials rotate every ~30 days.\n- **Secure deletion**: `biofs logout` overwrites credentials before unlinking.\n\n---\n\n## Development\n\n```bash\ngit clone git@github.com:Genobank/biofs-cli.git\ncd biofs-cli\nnpm install\nnpm run build                       # tsc → dist/\nnpm run dev -- stream my-wes        # run TypeScript directly\nnpm test                            # jest\nnpm link                            # global `biofs` → this checkout\n```\n\nArchitecture:\n\n```\nsrc/\n├── index.ts              # commander entry + command registration\n├── commands/             # one file per top-level command\n│   ├── stream.ts         # htsget stream → stdout\n│   ├── pipe.ts           # stream → bcftools/samtools view\n│   ├── alias.ts          # local shortcuts\n│   ├── htsget.ts         # low-level GA4GH endpoints\n│   ├── mount.ts          # {copy|nfs|fuse} dispatcher\n│   └── …\n├── lib/\n│   ├── api/client.ts     # GenoBankAPIClient (singleton)\n│   ├── auth/             # login + credentials\n│   ├── htsget/client.ts  # ticket fetcher\n│   ├── aliases/store.ts  # ~/.biofs/aliases.json\n│   ├── biofiles/         # resolver + downloader\n│   ├── context/          # .bionft manifest\n│   └── …\n└── types/                # shared type definitions\n```\n\nPull requests welcome. Code of conduct in `CONTRIBUTING.md`.\n\n---\n\n## License\n\n**AGPL-3.0-or-later** © GenoBank.io\n\nIf you deploy a modified version of BioFS as a service, you must make\nyour source available under the same license. See [`LICENSE`](LICENSE)\nfor the full text.\n\n---\n\n## Support\n\n- **Web**: <https://genobank.app/biofs>\n- **Docs**: <https://genobank.app/static/Genobank_API_Educational_Guide.html>\n- **GitHub**: <https://github.com/Genobank/biofs-cli>\n- **Security**: [security@genobank.io](mailto:security@genobank.io)\n- **General**: [support@genobank.io](mailto:support@genobank.io)\n","readmeFilename":"README.md"}