{"__v":26,"_id":"56268b769ef9ea0d00292356","category":{"__v":3,"_id":"55faf94b17b9d00d00969f47","pages":["56268b68b1c2630d00b112b2","56268b769ef9ea0d00292356","56d4984273dcd20b00fb86a9"],"project":"55faf11ba62ba1170021a9a7","version":"55faf11ba62ba1170021a9aa","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2015-09-17T17:32:59.805Z","from_sync":false,"order":12,"slug":"find-apps","title":"FIND APPS"},"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":"2015-10-20T18:44:06.670Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":1,"body":"Publicly available apps are maintained by the CGC bioinformatics team. There are currently more than 200 public apps, and new apps are constantly being added. You can search for an app by either entering the app name (e.g. \"SAMtools Index BAM\"), a part of the app description (e.g. \"sorted alignments for fast random access\"), or the toolkit (e.g. \"Samtools\").\n\nTo find a specific app:\n1. Navigate to the [public app gallery](doc:apps-on-the-cgc). \n2. Enter the desired keyword(s) (e.g. “somatic”) into the search field. \n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/GA4xZxiQTfitvxEXbwIc_pub-app4.jpg\",\n        \"pub-app4.jpg\",\n        \"1177\",\n        \"887\",\n        \"#2097c4\",\n        \"\"\n      ],\n      \"border\": true\n    }\n  ]\n}\n[/block]\n 3. To filter results based on the keyword, press **ENTER**. You will be presented with apps matching the search criteria (see below).\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/K8NuCch9Tde6KaN9OPqV_pub-app5.jpg\",\n        \"pub-app5.jpg\",\n        \"1154\",\n        \"906\",\n        \"#268db7\",\n        \"\"\n      ],\n      \"border\": true\n    }\n  ]\n}\n[/block]\n Here you can:\n\n* Filter further using the **Categories** filter. This would help you find apps based on the type of analysis involved (e.g. \"RNA\" or \"Alignment\").\n* Filter further based on **Toolkit** name (e.g. \"SamTools\") using the dropdown menu.\n* **Reset search** to start over.\n\nYou can view all of the tools and workflows matching your search criteria below the search panel.\n\n\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/bdWRkcubQ8qh1lP4dIkb_pub-app6.jpg\",\n        \"pub-app6.jpg\",\n        \"1097\",\n        \"746\",\n        \"#58779c\",\n        \"\"\n      ],\n      \"border\": true\n    }\n  ]\n}\n[/block]\nHere you can:\n1. Identify the type of an app.  <img src=\"https://files.readme.io/DiAAlV9aSHm0Dg5yNtGB_W-for-workflow.png\"\nheight=\"20px\" width=\"auto\" align=\"inline\" style=\"margin:1px\"/> denotes a Workflow and <img src=\"https://files.readme.io/LSAeDeOTIm5uSWCZ97bJ_T-for-tool.png\"\nheight=\"20px\" width=\"auto\" align=\"inline\" style=\"margin:1px\"/>  denotes a Tool.\n2. Read the App description.  \n3. Review **Toolkit** name and **Tool Versions**. If there is more than one version available for an app, you can choose a specific version from the dropdown menu.\n4. Review the categories to which the app belongs. You can click on the category to filter apps based on that category.\n5. Click **Details** to display details about an app, such as who created it and when.\n6. Click **Copy** to [copy this app into your project](doc:copy-an-app-from-a-project). Use this option if you'd like to edit your app.\n7. Click **Run** to [create a draft task](doc:set-up-a-task). Use this option if you'd like to run the app without editing it.\n\nTo get [more details about an ap](doc:explore-app-details)p, you can click the app name.","excerpt":"","slug":"search-for-an-app","type":"basic","title":"Search for an app"}
Publicly available apps are maintained by the CGC bioinformatics team. There are currently more than 200 public apps, and new apps are constantly being added. You can search for an app by either entering the app name (e.g. "SAMtools Index BAM"), a part of the app description (e.g. "sorted alignments for fast random access"), or the toolkit (e.g. "Samtools"). To find a specific app: 1. Navigate to the [public app gallery](doc:apps-on-the-cgc). 2. Enter the desired keyword(s) (e.g. “somatic”) into the search field. [block:image] { "images": [ { "image": [ "https://files.readme.io/GA4xZxiQTfitvxEXbwIc_pub-app4.jpg", "pub-app4.jpg", "1177", "887", "#2097c4", "" ], "border": true } ] } [/block] 3. To filter results based on the keyword, press **ENTER**. You will be presented with apps matching the search criteria (see below). [block:image] { "images": [ { "image": [ "https://files.readme.io/K8NuCch9Tde6KaN9OPqV_pub-app5.jpg", "pub-app5.jpg", "1154", "906", "#268db7", "" ], "border": true } ] } [/block] Here you can: * Filter further using the **Categories** filter. This would help you find apps based on the type of analysis involved (e.g. "RNA" or "Alignment"). * Filter further based on **Toolkit** name (e.g. "SamTools") using the dropdown menu. * **Reset search** to start over. You can view all of the tools and workflows matching your search criteria below the search panel. [block:image] { "images": [ { "image": [ "https://files.readme.io/bdWRkcubQ8qh1lP4dIkb_pub-app6.jpg", "pub-app6.jpg", "1097", "746", "#58779c", "" ], "border": true } ] } [/block] Here you can: 1. Identify the type of an app. <img src="https://files.readme.io/DiAAlV9aSHm0Dg5yNtGB_W-for-workflow.png" height="20px" width="auto" align="inline" style="margin:1px"/> denotes a Workflow and <img src="https://files.readme.io/LSAeDeOTIm5uSWCZ97bJ_T-for-tool.png" height="20px" width="auto" align="inline" style="margin:1px"/> denotes a Tool. 2. Read the App description. 3. Review **Toolkit** name and **Tool Versions**. If there is more than one version available for an app, you can choose a specific version from the dropdown menu. 4. Review the categories to which the app belongs. You can click on the category to filter apps based on that category. 5. Click **Details** to display details about an app, such as who created it and when. 6. Click **Copy** to [copy this app into your project](doc:copy-an-app-from-a-project). Use this option if you'd like to edit your app. 7. Click **Run** to [create a draft task](doc:set-up-a-task). Use this option if you'd like to run the app without editing it. To get [more details about an ap](doc:explore-app-details)p, you can click the app name.