Run a tool

Records

Everything you work on is a record in the data panel: a file you dropped, a folder you added, a built-in example, or a file that sits in the runner's workspace. A record knows its format (VCF, SBS-96 matrix, exposure table, Add object JSON, SNV table, CN segments, …), and that is what decides which functions it can feed.

Drop files anywhere in the studio, use the add buttons at the top of the data panel, or open an example. The eight example cohorts and the Tau example need nothing from you.

Functions

The Start tab lists every function with what it accepts and what is missing from your selection. Tick the records, then press Run on the function, or open it from the command palette (⌘K or Ctrl+K). A function opens in its own tab, bound to the records it was given; Change in the inputs box rebinds it.

| Function | Runs | Takes | |---|---|---| | Plot SNV spectrum | in the page | SBS-96 matrix, VCF, MAF | | Compare exposures | in the page | exposure tables | | SigMA2 curate | in the page | Add object JSON, or an exposure table with an SBS-96 matrix | | MuTopia | on the runner | somatic VCF and a reference FASTA | | MuSiCal | on the runner | SBS-96 matrix, or VCFs with context | | Tau | on the runner | SNV table with read counts and a CN table | | SigMA2 build, simulate, tune | on the runner | a VCF folder on the runner with an exposure table, or an Add object |

A function that runs in the page does its computing in a background worker of your browser, not in the page itself: Compare spectra resamples its pairs, Refit confidence runs its bootstrap, Map onto PCAWG scores a cohort while you keep scrolling, typing and switching tabs. The tool says where it is ("Resampling pair 120 of 276…"), closing or re-binding its tab stops the work, and a result is kept while the studio is open, so a tab opened again shows it at once. Nothing about this leaves your browser.

A step on the runner

A runner tool is a pipeline of steps, one Run button each, with the step's parameters beside the button. Pressing Run uploads what the step needs (or passes the path of something already on the runner), submits the job, and streams its log under the button. The first run of a tool also installs that tool's environment; the log shows it.

While the daemon is not there, the button is off and the words beside it say why: No runner, Runner stopped, Runner refused the token, Runner outdated, each with a link to the way in. The tool's checks in the inspector carry the same finding.

Results

When a run finishes, the stage reads what the package wrote and draws it. Nothing is recomputed in the page: the numbers are the package's. Every run stays listed under its step; see Runs, checkpoints, export.