{"__v":16,"_id":"5734cacbf48d550e00537f27","category":{"__v":1,"_id":"55faf99fa62ba1170021a9b9","pages":["5627e27c88948617002a097b"],"project":"55faf11ba62ba1170021a9a7","version":"55faf11ba62ba1170021a9aa","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2015-09-17T17:34:23.911Z","from_sync":false,"order":23,"slug":"developer-tools","title":"DEVELOPER TOOLS"},"parentDoc":null,"project":"55faf11ba62ba1170021a9a7","user":"5613e4f8fdd08f2b00437620","version":{"__v":37,"_id":"55faf11ba62ba1170021a9aa","project":"55faf11ba62ba1170021a9a7","createdAt":"2015-09-17T16:58:03.490Z","releaseDate":"2015-09-17T16:58:03.490Z","categories":["55faf11ca62ba1170021a9ab","55faf8f4d0e22017005b8272","55faf91aa62ba1170021a9b5","55faf929a8a7770d00c2c0bd","55faf932a8a7770d00c2c0bf","55faf94b17b9d00d00969f47","55faf958d0e22017005b8274","55faf95fa8a7770d00c2c0c0","55faf96917b9d00d00969f48","55faf970a8a7770d00c2c0c1","55faf98c825d5f19001fa3a6","55faf99aa62ba1170021a9b8","55faf99fa62ba1170021a9b9","55faf9aa17b9d00d00969f49","55faf9b6a8a7770d00c2c0c3","55faf9bda62ba1170021a9ba","5604570090ee490d00440551","5637e8b2fbe1c50d008cb078","5649bb624fa1460d00780add","5671974d1b6b730d008b4823","5671979d60c8e70d006c9760","568e8eef70ca1f0d0035808e","56d0a2081ecc471500f1795e","56d4a0adde40c70b00823ea3","56d96b03dd90610b00270849","56fbb83d8f21c817002af880","573c811bee2b3b2200422be1","576bc92afb62dd20001cda85","5771811e27a5c20e00030dcd","5785191af3a10c0e009b75b0","57bdf84d5d48411900cd8dc0","57ff5c5dc135231700aed806","5804caf792398f0f00e77521","58458b4fba4f1c0f009692bb","586d3c287c6b5b2300c05055","58ef66d88646742f009a0216","58f5d52d7891630f00fe4e77"],"is_deprecated":false,"is_hidden":false,"is_beta":true,"is_stable":true,"codename":"","version_clean":"1.0.0","version":"1.0"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-05-12T18:26:19.226Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":0,"body":"The CGC provides developer tools for researchers who want to retain all capabilities of the command line with the power of the CGC behind them.\n[block:callout]\n{\n  \"type\": \"success\",\n  \"title\": \"Authentication\",\n  \"body\": \"To set your CGC credentials, you will need to authenticate with [your authentication token](doc:get-your-authentication-token), which you can obtain from the developer dashboard.\"\n}\n[/block]\n#API\nThe CGC provides an API for integration and automation.\nUse the API to automate each step of an analysis for high throughput workflows.\n\n* <span style=\"color:gray\"><i>Read the [API Documentation](doc:the-cgc-api)</i></span>\n\n#SDK\nCGC's [Docker-based Software Development Kit](doc:sdk-overview) (SDK) lets you easily wrap your own tools and execute them on the CGC or anywhere that supports the Common Workflow Language.\n\n* <span style=\"color:gray\"><i>Read the [SDK Documentation](doc:sdk-overview)</i></span> \n* <span style=\"color:gray\"><i>Try the [SDK tutorial](doc:install-and-run-samtools-sort)</i></span>\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/Xro29jt1QEmmwg9xEYvw_cgc%20docker%20new%20(1).jpg\",\n        \"cgc docker new (1).jpg\",\n        \"1465\",\n        \"1402\",\n        \"#123cfb\",\n        \"\"\n      ],\n      \"border\": true,\n      \"sizing\": \"smart\",\n      \"caption\": \"Wrap and run your tools using Docker and the Seven Bridges SDK.\"\n    }\n  ]\n}\n[/block]\n\n[block:callout]\n{\n  \"type\": \"success\",\n  \"title\": \"The Common Workflow Language\",\n  \"body\": \"Both the SDK and the API read, write and run the Common Workflow Language (CWL), an open specification for data analysis workflows. The SDK [Tool Editor](doc:the-tool-editor) generates a CWL description of a tool, using information inputted to its graphical interface. The API reads and writes tool descriptions as JSON formatted CWL.\\n\\nLearn more about CWL on[ the CWL homepage](http://common-workflow-language.github.io/).\"\n}\n[/block]\n\n#Command Line Uploader\nThe CGC provides an upload client that runs from the command line. Use it to efficiently upload files from remote servers, or to incorporate file uploading into other workflows.\n\n* <span style=\"color:gray\"><i>Read the [Command Line Uploader documentation](doc:upload-via-the-command-line)</i></span>\n[block:callout]\n{\n  \"type\": \"info\",\n  \"title\": \"We always welcome feedback!\",\n  \"body\": \"If you have any questions, comments, or bug reports on the developer documentation please do not hesitate to contact us at [cgc:::at:::sbgenomics.com](mailto:cgc@sbgenomics.com).\"\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>","excerpt":"","slug":"developer-hub","type":"basic","title":"Developer Hub"}
The CGC provides developer tools for researchers who want to retain all capabilities of the command line with the power of the CGC behind them. [block:callout] { "type": "success", "title": "Authentication", "body": "To set your CGC credentials, you will need to authenticate with [your authentication token](doc:get-your-authentication-token), which you can obtain from the developer dashboard." } [/block] #API The CGC provides an API for integration and automation. Use the API to automate each step of an analysis for high throughput workflows. * <span style="color:gray"><i>Read the [API Documentation](doc:the-cgc-api)</i></span> #SDK CGC's [Docker-based Software Development Kit](doc:sdk-overview) (SDK) lets you easily wrap your own tools and execute them on the CGC or anywhere that supports the Common Workflow Language. * <span style="color:gray"><i>Read the [SDK Documentation](doc:sdk-overview)</i></span> * <span style="color:gray"><i>Try the [SDK tutorial](doc:install-and-run-samtools-sort)</i></span> [block:image] { "images": [ { "image": [ "https://files.readme.io/Xro29jt1QEmmwg9xEYvw_cgc%20docker%20new%20(1).jpg", "cgc docker new (1).jpg", "1465", "1402", "#123cfb", "" ], "border": true, "sizing": "smart", "caption": "Wrap and run your tools using Docker and the Seven Bridges SDK." } ] } [/block] [block:callout] { "type": "success", "title": "The Common Workflow Language", "body": "Both the SDK and the API read, write and run the Common Workflow Language (CWL), an open specification for data analysis workflows. The SDK [Tool Editor](doc:the-tool-editor) generates a CWL description of a tool, using information inputted to its graphical interface. The API reads and writes tool descriptions as JSON formatted CWL.\n\nLearn more about CWL on[ the CWL homepage](http://common-workflow-language.github.io/)." } [/block] #Command Line Uploader The CGC provides an upload client that runs from the command line. Use it to efficiently upload files from remote servers, or to incorporate file uploading into other workflows. * <span style="color:gray"><i>Read the [Command Line Uploader documentation](doc:upload-via-the-command-line)</i></span> [block:callout] { "type": "info", "title": "We always welcome feedback!", "body": "If you have any questions, comments, or bug reports on the developer documentation please do not hesitate to contact us at [cgc@sbgenomics.com](mailto:cgc@sbgenomics.com)." } [/block] <div align="right"><a href="#top">top</a></div>