From 6711d2b8cc1dfdce81febe415299a486e39550d2 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 9 Dec 2024 13:41:49 +0000 Subject: [PATCH 1/2] Bump d3-color and @jbrowse/plugin-wiggle in /beaconplusWeb Bumps [d3-color](https://github.com/d3/d3-color) and [@jbrowse/plugin-wiggle](https://github.com/GMOD/jbrowse-components/tree/HEAD/plugins/wiggle). These dependencies needed to be updated together. Updates `d3-color` from 2.0.0 to 3.1.0 - [Release notes](https://github.com/d3/d3-color/releases) - [Commits](https://github.com/d3/d3-color/compare/v2.0.0...v3.1.0) Updates `@jbrowse/plugin-wiggle` from 2.11.1 to 2.17.0 - [Release notes](https://github.com/GMOD/jbrowse-components/releases) - [Changelog](https://github.com/GMOD/jbrowse-components/blob/main/CHANGELOG.md) - [Commits](https://github.com/GMOD/jbrowse-components/commits/v2.17.0/plugins/wiggle) --- updated-dependencies: - dependency-name: d3-color dependency-type: indirect - dependency-name: "@jbrowse/plugin-wiggle" dependency-type: indirect ... Signed-off-by: dependabot[bot] --- beaconplusWeb/package-lock.json | 831 ++++++++++++++------------------ 1 file changed, 352 insertions(+), 479 deletions(-) diff --git a/beaconplusWeb/package-lock.json b/beaconplusWeb/package-lock.json index fa6954f87..f0129bea5 100644 --- a/beaconplusWeb/package-lock.json +++ b/beaconplusWeb/package-lock.json @@ -14,7 +14,6 @@ "@tippyjs/react": "^4.2.0", "animate": "^1.0.0", "animate.css": "^4.1.1", - "build": "^0.1.4", "classnames": "^2.2.6", "env-cmd": "^10.1.0", "file-saver": "^2.0.5", @@ -472,9 +471,9 @@ } }, "node_modules/@babel/runtime": { - "version": "7.24.5", - "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.24.5.tgz", - "integrity": "sha512-Nms86NXrsaeU9vbBJKni6gXiEXZ4CVpYVzEjDH9Sb8vmZ3UljyA1GSOJl/6LGPO8EHLuSF9H+IxNXHPX8QHJ4g==", + "version": "7.26.0", + "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.26.0.tgz", + "integrity": 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"sha512-l4Sp/DRseor9wL6EvV2+TuQn63dMkPjZ/sp9XkghTEbV9KlPS1xUsZ3u7/IQO4wxtcFB4bgpQPRcR3QCvezPcQ==", "dev": true }, - "node_modules/wrench": { - "version": "1.3.9", - "resolved": "https://registry.npmjs.org/wrench/-/wrench-1.3.9.tgz", - "integrity": "sha512-srTJQmLTP5YtW+F5zDuqjMEZqLLr/eJOZfDI5ibfPfRMeDh3oBUefAscuH0q5wBKE339ptH/S/0D18ZkfOfmKQ==", - "deprecated": "wrench.js is deprecated! You should check out fs-extra (https://github.com/jprichardson/node-fs-extra) for any operations you were using wrench for. Thanks for all the usage over the years.", - "engines": { - "node": ">=0.1.97" - } - }, "node_modules/write-file-atomic": { "version": "3.0.3", "resolved": "https://registry.npmjs.org/write-file-atomic/-/write-file-atomic-3.0.3.tgz", From f330d24f194b5b02da6ebcb100b658b1dc326642 Mon Sep 17 00:00:00 2001 From: Michael Baudis Date: Mon, 9 Dec 2024 14:53:35 +0100 Subject: [PATCH 2/2] Update beaconplus.md --- docs/beaconplus.md | 36 ++++++++++++++++++++++++++++++++++-- 1 file changed, 34 insertions(+), 2 deletions(-) diff --git a/docs/beaconplus.md b/docs/beaconplus.md index 5e02885e3..b43cadf5b 100644 --- a/docs/beaconplus.md +++ b/docs/beaconplus.md @@ -1,7 +1,7 @@ # BeaconPlus - Beacon Front-end for Genomic Data Queries ![Beacon Icon](http://docs.progenetix.org/img/logo_beacon.png){ align=right width=25px} As part of the Beacon project, since early 2016 the [Theoretical Cytogenetics and Oncogenomics Group](http://info.baudisgroup.org) at the University of Zurich develops the -[Beacon+ demonstrator](https://beacon.progenetix.org/ui/), +[Beacon+ demonstrator](https://beaconplus.progenetix.org/), to show current functionality and test future Beacon protocol extensions. The Beacon+ implementation is a @@ -10,11 +10,43 @@ code with emphasis on structural genome variations from cancer samples. An extended implementation of the Beacon+ code is provided through the [Progenetix](https://progenetix.org) project.s -!!! note "Technical Documentation" +!!! note "More Documentation" The documentation relevant to the API can be found in these locations: * [`bycon` package documentation](http://bycon.progenetix.org) * Beacon v2 [documentation site](http://docs.genomebeacons.org) +## Installation +The project code for the BeaconPlus front end lives inside `bycon/beaconplusWeb` +and is tested as a static compiled React project (YMMV ...). + +### Configuration + +Please edit the target installation directory `server_site_dir_loc` in the +`local/local_paths.yaml` configuration file. + +Adjustments to dataset definitions etc. being used by the front end are in +`bycon/beaconplusWeb/src/config.js`. + +Additionally runtime variables for server name etc. should be set in the environmental +definitions in `bycon/beaconplusWeb/env`. + +### Compile & Install + +The developer runner `updev.sh` also calls the `install.py` script which asks +for installation of the front end. It boils down to + +```bash +cd bycon/beaconplusWeb +npm run local +``` +... for local test installations or + +```bash +cd bycon/beaconplusWeb +npm run update +``` +... for the outside facing server one (YMMV; these just invoke different settings +defined in `bycon/beaconplusWeb/env`). \ No newline at end of file