Sync Apps docs with the fileglancer more-apps PR#22
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…uffix Document that auto_url now publishes the URL only once the port is accepting connections, the new FG_SERVICE_TOKEN env var, and the service_url_suffix template for one-click token URLs. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
The apps UI was reworked: cards are clickable with a banner (type icon, Launch button, actions menu) and the app info dialog was replaced by a detail page; the catalog got the same treatment with a listing detail page; the launch and job detail pages moved under the apps tabs with a shared back-arrow header. Update the guide accordingly: Add from URL/Continue dialog flow, the app detail page section (replacing App Info), actions-menu wording for update/remove/share, catalog Add and listing detail page, and the job detail header/overview description. Remove the info-icon and info-dialog screenshots since that UI no longer exists; also drop the listing-edit claim, which has no UI. Remaining screenshots predate the redesign and should be retaken. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…ob checkouts Fileglancer apps are now pinned to an exact commit when added: jobs run from an immutable per-commit checkout instead of a shared mutable clone, updates move only the targeted app's pin (siblings in the same repo and running jobs are unaffected), an "Update available" tag flags apps whose source has newer commits, and job detail pages record the commit each job executed. Update the user guide and authoring pages to match. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…params Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…st validation - Document the new value_separator (space/equals) and boolean_style (flag/value) parameter fields and their effect on command building. - Note that optional flagged parameters with an empty value are omitted entirely rather than emitted as --flag ''. - Describe the Nextflow-safe forms forced at command-build time for 'nextflow run' commands (equals separator, explicit booleans). - Tighten the flag field description to the conservative CLI-flag pattern now enforced (one or two dashes, then letters/digits/_/./-). - repo_url must parse as a GitHub URL and runnables requires at least one entry; both are now rejected at manifest load time.
…on fixes - Nextflow apps are now named by repository only (rnaseq), not org/repo. - Pipeline parameters emit --flag=value and explicit --flag=true/false, applied at command-build time so older cached manifests are fixed too; update the example command accordingly (extra args go at the end). - Correct the Pixi naming rule: project metadata name first, then the Git repository name.
…bind sources - Document the new apps.worker_env_passthrough setting and the allowlisted worker environment (FGC_* never passed through). - Document apps.unknown_timeout_hours and the UNKNOWN status lifecycle from the admin's perspective. - Note that ~/ container cache paths are expanded to the user's home. - Clarify that container bind mounts come from the effective parameter values — manifest defaults and env_parameters included.
…ting edits - Add a caution that apps run repository code as the user, shown when adding from a URL or the catalog. - Document the UNKNOWN job status (treated as active, cancellable, not deletable) and the 24h default cutoff, plus a troubleshooting entry. - New 'Deleting a Job' section: deletion removes the job's entire working directory including logs, behind a confirmation dialog. - Note that large logs display only the trailing 5 MB and the full file is reachable through the file browser. - Catalog: add-confirmation dialog shows source/sharer/date, listings are editable after sharing, and unshare asks for confirmation. - Extra scheduler arguments are shell-tokenized (LSF resource strings work); relaunch preserves Environment-tab settings; launch-page install adds only the current app from a multi-app repo.
Co-authored-by: Codex <codex@openai.com>
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Updates the Apps user guide and the Authoring Apps developer docs to match the current state of the fileglancer more-apps PR.
User guide (Apps and Jobs)
-R "select[mem>8000]"work; relaunch preserves Environment-tab settings; launch-page install adds only the current app from a multi-app repoAuthoring guide
auto_url,FG_SERVICE_PORT/FG_HOSTNAME/FG_SERVICE_TOKEN,service_url_suffix, readiness-gated URL publishing, and the "Downloading container image…" startup messagevalue_separator(space/equals) andboolean_style(flag/value), with the Nextflow-safe forms forced fornextflow runcommandsexistson file/directory parameters (replacingcreate_if_missing), with pre-launch directory creation for outputsrepo_urlmust parse as a GitHub URL, manifests require at least one runnable--flag=valueemission with explicit booleans, corrected example and Pixi naming rulesworker_env_passthrough(allowlisted worker environment) andunknown_timeout_hourssettings, container cache~expansion@StephanPreibisch @JaneliaSciComp/fileglancer