{"id":20930679,"url":"https://github.com/intermine/intermine-steps","last_synced_at":"2025-07-21T18:36:02.299Z","repository":{"id":6390185,"uuid":"7627966","full_name":"intermine/intermine-steps","owner":"intermine","description":"InterMine 2.0 Prototype preserving history of Steps","archived":false,"fork":false,"pushed_at":"2014-02-12T17:50:06.000Z","size":5772,"stargazers_count":2,"open_issues_count":16,"forks_count":2,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-03-13T02:16:08.936Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"JavaScript","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/intermine.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2013-01-15T16:00:58.000Z","updated_at":"2017-01-20T16:53:34.000Z","dependencies_parsed_at":"2022-07-29T01:49:04.953Z","dependency_job_id":null,"html_url":"https://github.com/intermine/intermine-steps","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/intermine/intermine-steps","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/intermine%2Fintermine-steps","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/intermine%2Fintermine-steps/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/intermine%2Fintermine-steps/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/intermine%2Fintermine-steps/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/intermine","download_url":"https://codeload.github.com/intermine/intermine-steps/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/intermine%2Fintermine-steps/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":266352905,"owners_count":23915848,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-07-21T11:47:31.412Z","response_time":64,"last_error":null,"robots_txt_status":null,"robots_txt_updated_at":null,"robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-18T21:35:30.798Z","updated_at":"2025-07-21T18:36:02.275Z","avatar_url":"https://github.com/intermine.png","language":"JavaScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"# InterMine Steps\n\nInterMine 2.0 Prototype preserving history of Steps\n\n**[Questions \u0026 Answers](docs/q-n-a.md)**\n\n![image](https://raw.github.com/intermine/intermine-steps/master/example.png)\n\n##Install\n\n###Required Packages###\n\n####NPM\n\nMake sure you have [node.js](https://github.com/joyent/node/wiki/Installing-Node.js-via-package-manager) installed which installs its package manager, [npm](https://npmjs.org/), too.\n\n`node.js` version v0.6.19, currently supported on Ubuntu, is too old for `npm` to work. You have two options:\n\nYou can upgrade to the last release using npm itself (see [this page](http://davidwalsh.name/upgrade-nodejs))\n\n```bash\n$ sudo npm cache clean -f\n$ sudo npm install -g n\n$ sudo n stable\n```\n\nAlternatively, install `node.js` [from sources](https://github.com/joyent/node/wiki/Installing-Node.js-via-package-manager#debian-lmde).\n\n####Bower (optional)\n\nYou can skip this step if you just want to start an instance of Steps without making changes to it.\n\nThe app fetches a bunch of tools and their vendor dependencies, do so by using [Bower](http://bower.io/):\n\n```bash\n$ sudo npm install -g bower\n$ bower install\n```\n\nIt fetches libraries defined in the `bower.json` file. So, whenever you make changes to this file, you need to re-run the `bower install` command and the `grunt` command which we will discuss next.\n\n####Grunt (optional)\n\nYou can skip this step if you just want to start an instance of Steps without making changes to it.\n\nAnother tool we are using is [Grunt](http://gruntjs.com/) that builds Steps and munges the different tools and its deps into single builds. To [install Grunt](http://gruntjs.com/getting-started) and make a build:\n\n```bash\n$ sudo npm install -g grunt-cli\n$ grunt\n```\n\nThe build steps are defined in the file `Gruntfile.coffee`. Whever you make changes to this file, or whenever you make changes to the `/src` or `/tools` directory, you need to run a new build using the `grunt` command.\n\nWhen you are developing, it is recommended that you watch the default Grunt task like so:\n\n```bash\n$ watch --color grunt\n```\n###Steps###\n\nClone this repository\n\n`\ngit clone git@github.com:intermine/intermine-steps.git my-steps-directory\n`\n\nand install the app dependencies:\n\n```bash\n$ cd my-steps-directory\n$ npm install\n```\n\n\n##Startup\n\nNow we can startup Steps on a custom port and visit it in the browser.\n\nFrom your \u003cem\u003esteps\u003c/em\u003e directory\n\n```bash\n$ PORT=4444 coffee server/server.coffee\n```\n\nIf you need to get CoffeeScript `coffee` command, do the following step:\n\n```bash\n$ sudo npm install coffee-script -g\n```\n\nIf you need to install the module `flatiron`\n\n```bash\n$ sudo npm install flatiron -g\n```\n\n\n##Configuration\n\nThe default tools configuration is in `tools/config.coffee`.\n\u003c!--\n\nTo change the application to point to your InterMine of interest, please edit line #4 of the file\n\n```\n     'mine': 'http://www.flymine.org/'\n```\n--\u003e\n\n#### Registry of tools labels ####\n\nYou will also find a registry of tool labels that will show up in various scenarios.\n\nFor example:\n\n```coffeescript\n{\n    'label': 'mRNA subcellular localisation (fly-FISH)'\n    'weight': 10\n    'context': [ 'have:list', 'type:Gene' ]\n    'place': 'right'\n    'category': [ 'Category 1' ]\n    'extra': [ 'chart', 'flyfish' ]\n}\n```\n\nwith\n\n\u003ctable\u003e\n    \u003ctr\u003e\n        \u003cth\u003elabel\u003c/th\u003e\n        \u003ctd\u003eThis is the label that will show up in a menu. All the text from this label is\n        searchable.\u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n        \u003cth\u003eweight\u003c/th\u003e\n        \u003ctd\u003eWill determine the order in which labels will show. Higher number means higher\n        position. Labels below \u003cem\u003e10\u003c/em\u003e do not initially show in a menuand one needs to\n        click a button to expand the menu and show these.\u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n        \u003cth\u003econtext\u003c/th\u003e\n        \u003ctd\u003eThis label will show up when all of the context rules are met. The rules are just\n        messages triggered by currently running tools.\u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n        \u003cth\u003eplace\u003c/th\u003e\n        \u003ctd\u003eIn which menu is this label to appear?\u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n        \u003cth\u003ecategory\u003c/th\u003e\n        \u003ctd\u003eAn array allowing you to create a nested structure where your label will appear.\u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n        \u003cth\u003eextra\u003c/th\u003e\n        \u003ctd\u003eParameters passed to a tool to differentiate between variants of it.\u003c/td\u003e\n    \u003c/tr\u003e\n\u003c/table\u003e","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fintermine%2Fintermine-steps","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fintermine%2Fintermine-steps","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fintermine%2Fintermine-steps/lists"}