sigscape-daemon reference

Command line

sigscape-daemon [--workspace DIR] [--studio URL] [--open]
                [--allow-origin URL]... [--port N] [--token T] [--jobs N]
sigscape-daemon update
sigscape-daemon --version

| Flag | Meaning | Default | |---|---|---| | --workspace DIR | the folder for uploads, runs and data | the current directory | | --studio URL | the site the printed link opens | https://sigscape.org | | --open | open the link in a browser | off | | --allow-origin URL | admit another page origin, for a dev server | none | | --port N | listen on this port | a free one | | --token T | use this token instead of a fresh one | fresh each start | | --jobs N | how many jobs run at once | 2 | | update | install the latest release in place | |

Environment: SIGSCAPE_GITHUB_TOKEN (or GITHUB_TOKEN, GH_TOKEN) for the private releases; SIGSCAPE_UPDATE_BASE points the updater at a staged release folder for testing; SIGSCAPE_<TOOL>_SRC installs a tool from a local checkout.

Workspace

<workspace>/
  uploads/            files the page sent
  data/               what you put there; listed as records
  sigscape-runs/<id>/ one folder per run: outputs, job.json, daemon.log

HTTP API

All routes take Authorization: Bearer <token> or ?token=. The daemon listens on 127.0.0.1 only.

| Route | What | |---|---| | GET /api/status | version, API version, platform, workspace, tools, jobs in flight, runs kept, the last release check | | GET /api/tools | each tool's inputs and parameters | | GET /api/files | every file in the workspace | | GET /api/files/{path} | a range of a file; PUT lands an upload under uploads/ | | POST /api/jobs/validate | the problems a request would have, without running it | | POST /api/jobs | submit {tool, inputs, params, meta}; returns the job id | | GET /api/jobs | every job, including those earlier daemons left in the workspace | | GET /api/jobs/{id}/events | the job's state and log as server-sent events | | POST /api/jobs/{id}/cancel | stop it | | GET /api/jobs/{id}/artifacts | the files it wrote; /artifacts/{path} reads one | | GET /api/jobs/{id}/export | the run folder as a zip; GET /api/export?jobs=a,b zips several | | GET /api/update | the latest release against the running version | | POST /api/update | download, verify, swap the binary, restart on the same address | | POST /api/restart | restart on the same address | | GET /api/log | what the daemon said since it started |

Tools and their stages

| Tool | Stages | Reads | |---|---|---| | musical | discover, match, refit | an SBS-96 matrix; later stages read earlier runs by path | | tau | run | an SNV table and a CN table | | mutopia | annotate | a VCF and a reference FASTA | | sigma2 | build, simulate, tune | a VCF folder with an exposure table, then the earlier run's pickle; or an Add object JSON for tune alone |