{"__v":25,"_id":"56268b3cc2781f0d00364bc0","category":{"__v":8,"_id":"55faf958d0e22017005b8274","pages":["56268b3cc2781f0d00364bc0","5637bfa84dbdd919001b277d","5637e6fe97666c0d008656b6","5637e74acfaa870d00cdeb7a","5637e764f7e3990d007b2c52","5640baf604c3eb0d006fc43c","56cccb6894c8f00b00b83f24","56ddf68dba70f50e0033c6df"],"project":"55faf11ba62ba1170021a9a7","version":"55faf11ba62ba1170021a9aa","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2015-09-17T17:33:12.687Z","from_sync":false,"order":13,"slug":"bring-your-tools","title":"BRING YOUR 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":["5649ed773242592b00338a01","56697ef607625117002c27da"],"next":{"pages":[],"description":""},"createdAt":"2015-10-20T18:43:08.748Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":0,"body":"You can put tools that you have developed yourself onto the CGC, for on demand access to elastic computational resources and large data repositories like TCGA. \n\nThe CGC Software Development Kit (SDK) is called Rabix. It allows you to wrap your tools so that they can be executed on the CGC. This is done in a way that renders the tools fully portable, by first installing them inside Docker containers and then describing their behavior in accordance with the Common Workflow Language.\n\nThis means that there is no need to reconfigure your existing command line tools to meet any proprietary format, or write a wrapper for them. Additionally, the tools remain runnable across a diverse range of infrastructures should you want to use them on different platforms.\n\n##DOCKER\nYou can use [Docker](doc:docker-basics) to build and run Docker containers containing your tools, along with their dependencies. Then, you can push snapshots of these containers, called images, to the [CGC Image Registry](doc:the-cgc-image-registry), which is housed on our computational platform, or to Docker hub – Docker's own image registry. The tools you have installed will be run inside the containers on the CGC.\n\n##The Tool Editor\nHaving uploaded a Docker image containing your tool to the image registry, you can specify its behavior, including its inputs and outputs, runtime requirements, and execution semantics. The specification is entered using the [Tool Editor](doc:the-tool-editor). It allows the tool to be used on the CGC to interface with other arbitrary tools.\n\n##The Common Workflow Language\nThe specification of your tool that you enter using the [Tool Editor](doc:the-tool-editor) will be automatically transcribed into the Common Workflow Language (CWL). This is a community developed, open specification for bioinformatics workflows.\n\nWorkflows constructed on the CGC can also be described using the CWL. This supports reproducibility of workflows in two ways:\n\n**1. CWL specifications are exhaustive:**\n\nThe CWL specifies all configurable details of a workflow execution, right down to each tool's parameterization and the configuration of the environment in which the tools are executed.\nThis information is provided and stored for every workflow you run on the CGC. It allows you to easily reference any results obtained, and to provide colleagues with all the information they need to run identical executions.\n\n**2. CWL specifications are platform-agnostic:**\n\nSince the CWL is an open specification, workflows described using it can be executed on any platform that supports the specification.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/6JktbwtSw6eiyHLxZet6_cgc%20docker%20new.jpg\",\n        \"cgc docker new.jpg\",\n        \"1465\",\n        \"1402\",\n        \"#123cfb\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\n\n[block:callout]\n{\n  \"type\": \"success\",\n  \"body\": \"If you are familiar with the Common Workflow Language you are free to upload your own Common Workflow Language description of the tool's behavior.\",\n  \"title\": \"An alternative to the Tool Editor:\"\n}\n[/block]","excerpt":"Wrap and run tools with Rabix","slug":"sdk-overview","type":"basic","title":"Rabix Overview"}

Rabix Overview

Wrap and run tools with Rabix

You can put tools that you have developed yourself onto the CGC, for on demand access to elastic computational resources and large data repositories like TCGA. The CGC Software Development Kit (SDK) is called Rabix. It allows you to wrap your tools so that they can be executed on the CGC. This is done in a way that renders the tools fully portable, by first installing them inside Docker containers and then describing their behavior in accordance with the Common Workflow Language. This means that there is no need to reconfigure your existing command line tools to meet any proprietary format, or write a wrapper for them. Additionally, the tools remain runnable across a diverse range of infrastructures should you want to use them on different platforms. ##DOCKER You can use [Docker](doc:docker-basics) to build and run Docker containers containing your tools, along with their dependencies. Then, you can push snapshots of these containers, called images, to the [CGC Image Registry](doc:the-cgc-image-registry), which is housed on our computational platform, or to Docker hub – Docker's own image registry. The tools you have installed will be run inside the containers on the CGC. ##The Tool Editor Having uploaded a Docker image containing your tool to the image registry, you can specify its behavior, including its inputs and outputs, runtime requirements, and execution semantics. The specification is entered using the [Tool Editor](doc:the-tool-editor). It allows the tool to be used on the CGC to interface with other arbitrary tools. ##The Common Workflow Language The specification of your tool that you enter using the [Tool Editor](doc:the-tool-editor) will be automatically transcribed into the Common Workflow Language (CWL). This is a community developed, open specification for bioinformatics workflows. Workflows constructed on the CGC can also be described using the CWL. This supports reproducibility of workflows in two ways: **1. CWL specifications are exhaustive:** The CWL specifies all configurable details of a workflow execution, right down to each tool's parameterization and the configuration of the environment in which the tools are executed. This information is provided and stored for every workflow you run on the CGC. It allows you to easily reference any results obtained, and to provide colleagues with all the information they need to run identical executions. **2. CWL specifications are platform-agnostic:** Since the CWL is an open specification, workflows described using it can be executed on any platform that supports the specification. [block:image] { "images": [ { "image": [ "https://files.readme.io/6JktbwtSw6eiyHLxZet6_cgc%20docker%20new.jpg", "cgc docker new.jpg", "1465", "1402", "#123cfb", "" ] } ] } [/block] [block:callout] { "type": "success", "body": "If you are familiar with the Common Workflow Language you are free to upload your own Common Workflow Language description of the tool's behavior.", "title": "An alternative to the Tool Editor:" } [/block]