{"_id":"56f999ce320d6834008830c4","user":"5613e4f8fdd08f2b00437620","__v":15,"parentDoc":null,"project":"55faf11ba62ba1170021a9a7","version":{"_id":"55faf11ba62ba1170021a9aa","project":"55faf11ba62ba1170021a9a7","__v":38,"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","59a555bccdbd85001bfb1442"],"is_deprecated":false,"is_hidden":false,"is_beta":true,"is_stable":true,"codename":"","version_clean":"1.0.0","version":"1.0"},"category":{"_id":"55faf96917b9d00d00969f48","pages":["5626a5d644c87f0d00fe6396","5626a5e4e2ce610d004e3dd8","5626a89ce2ce610d004e3dde","56429a87f49bfa0d002f54e0"],"project":"55faf11ba62ba1170021a9a7","__v":4,"version":"55faf11ba62ba1170021a9aa","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2015-09-17T17:33:29.016Z","from_sync":false,"order":18,"slug":"run-an-analysis","title":"RUN AN ANALYSIS"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-03-28T20:53:34.168Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":2,"body":"Many bioinformatics tools and workflows require reference genomes and annotation files to work properly. The CGC hosts the latest and the most frequently used reference genomes and annotation files in its **Public Reference Files** repository, so you won't have to upload your own reference files each time.\n[block:callout]\n{\n  \"type\": \"success\",\n  \"body\": \"To help you get started with your analyses, the CGC maintains public workflows in the **Public apps** gallery. Specific public reference files are linked to a CGC public workflow as \\\"suggested files\\\". A **Suggested files** pop-up will prompt you to add the suggested files while setting up your [draft task](doc:set-up-a-task).\\n\\nThese suggested files allow you to easily select the necessary reference files to help your workflow run properly. See below for more on adding public reference files to your task.\",\n  \"title\": \"Suggested files\"\n}\n[/block]\nTo select public reference files for your task:  \n \n1. First [copy all required reference files](doc:copy-files-to-a-project) to your project.\n2. Then, prepare your **DRAFT** task by [navigating to your desired project](view-a-project) and selecting the **Apps** tab in your project.\n3. On the **Apps** page, click the run icon <img src=\"https://files.readme.io/o3vzUJkTTEybiiKrA6k7_Screen%20Shot%202016-03-09%20at%205.34.22%20PM.png\"\nheight=\"20px\" width=\"auto\" align=\"inline\" style=\"margin:1px\"/> next to to the public workflow.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/tCi2ITVSjaTBZiji88Fe_Screen%20Shot%202016-03-28%20at%205.00.28%20PM.jpeg\",\n        \"Screen Shot 2016-03-28 at 5.00.28 PM.jpeg\",\n        \"2362\",\n        \"726\",\n        \"#165390\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\n4. The **Select Input Data** tab on the **DRAFT** task page contains fields which require reference files as inputs. In the image below, the **RNA-seq Alignment - STAR** workflow uses a reference genome (**ucsc.hg19.fasta**) and an optional transcript annotation file (**uman_hg19_genes_2014.gtf**) to map RNA-Seq reads. \n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/wpN8JvH9RpSfcG72IhrQ_Screen%20Shot%202016-04-11%20at%205.19.05%20PM%20(1).jpeg\",\n        \"Screen Shot 2016-04-11 at 5.19.05 PM (1).jpeg\",\n        \"2838\",\n        \"1420\",\n        \"#175291\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\n5. Click **Pick files** to choose these public reference files.\n \nOnce you have added all the [input](select-input-files) and reference files, you can set your app's parameters and execute the task.\n\n##Suggested Files\n \nTo help you get started with your analyses, some of the Seven Bridges public workflows in the **Public apps** gallery have suggested reference files. A **Suggested files** pop-up will prompt you to add the suggested files while setting up your [draft task](doc:set-up-a-task). These suggested files allow you to easily select the necessary reference files to help your workflow run properly.\n \nIf any of your workflow's suggested files are not in your project, a **Suggested files** pop-up will prompt you to copy the missing files to your project. You can:\n \n  * Click **Copy** to populate your task with the suggested files.\n  * Click **Don’t copy** to ignore the suggested files, permanently dismiss this pop-up, and choose your own. None of the suggested files will be copied, and this window will not be displayed again.\n  * Click **X** to postpone your decision. The **Suggested files** pop-up will appear again the next time you access this task.\n\nIf you already have all the suggested reference files for a workflow in your project, they will pre-populate your draft task page, and you won't be prompted to copy them.\n\n[block:callout]\n{\n  \"type\": \"info\",\n  \"body\": \"To select a reference file other than the suggested files, click **Pick Files** and choose any other files in your project.\",\n  \"title\": \"Choosing a different reference file\"\n}\n[/block]\n\nOnce you have added all the [input](select-input-files) and reference files, you can [set your app's parameters](define-app-settings) and execute the task.","excerpt":"","slug":"select-reference-files","type":"basic","title":"Select Reference Files"}

Select Reference Files


Many bioinformatics tools and workflows require reference genomes and annotation files to work properly. The CGC hosts the latest and the most frequently used reference genomes and annotation files in its **Public Reference Files** repository, so you won't have to upload your own reference files each time. [block:callout] { "type": "success", "body": "To help you get started with your analyses, the CGC maintains public workflows in the **Public apps** gallery. Specific public reference files are linked to a CGC public workflow as \"suggested files\". A **Suggested files** pop-up will prompt you to add the suggested files while setting up your [draft task](doc:set-up-a-task).\n\nThese suggested files allow you to easily select the necessary reference files to help your workflow run properly. See below for more on adding public reference files to your task.", "title": "Suggested files" } [/block] To select public reference files for your task: 1. First [copy all required reference files](doc:copy-files-to-a-project) to your project. 2. Then, prepare your **DRAFT** task by [navigating to your desired project](view-a-project) and selecting the **Apps** tab in your project. 3. On the **Apps** page, click the run icon <img src="https://files.readme.io/o3vzUJkTTEybiiKrA6k7_Screen%20Shot%202016-03-09%20at%205.34.22%20PM.png" height="20px" width="auto" align="inline" style="margin:1px"/> next to to the public workflow. [block:image] { "images": [ { "image": [ "https://files.readme.io/tCi2ITVSjaTBZiji88Fe_Screen%20Shot%202016-03-28%20at%205.00.28%20PM.jpeg", "Screen Shot 2016-03-28 at 5.00.28 PM.jpeg", "2362", "726", "#165390", "" ] } ] } [/block] 4. The **Select Input Data** tab on the **DRAFT** task page contains fields which require reference files as inputs. In the image below, the **RNA-seq Alignment - STAR** workflow uses a reference genome (**ucsc.hg19.fasta**) and an optional transcript annotation file (**uman_hg19_genes_2014.gtf**) to map RNA-Seq reads. [block:image] { "images": [ { "image": [ "https://files.readme.io/wpN8JvH9RpSfcG72IhrQ_Screen%20Shot%202016-04-11%20at%205.19.05%20PM%20(1).jpeg", "Screen Shot 2016-04-11 at 5.19.05 PM (1).jpeg", "2838", "1420", "#175291", "" ] } ] } [/block] 5. Click **Pick files** to choose these public reference files. Once you have added all the [input](select-input-files) and reference files, you can set your app's parameters and execute the task. ##Suggested Files To help you get started with your analyses, some of the Seven Bridges public workflows in the **Public apps** gallery have suggested reference files. A **Suggested files** pop-up will prompt you to add the suggested files while setting up your [draft task](doc:set-up-a-task). These suggested files allow you to easily select the necessary reference files to help your workflow run properly. If any of your workflow's suggested files are not in your project, a **Suggested files** pop-up will prompt you to copy the missing files to your project. You can: * Click **Copy** to populate your task with the suggested files. * Click **Don’t copy** to ignore the suggested files, permanently dismiss this pop-up, and choose your own. None of the suggested files will be copied, and this window will not be displayed again. * Click **X** to postpone your decision. The **Suggested files** pop-up will appear again the next time you access this task. If you already have all the suggested reference files for a workflow in your project, they will pre-populate your draft task page, and you won't be prompted to copy them. [block:callout] { "type": "info", "body": "To select a reference file other than the suggested files, click **Pick Files** and choose any other files in your project.", "title": "Choosing a different reference file" } [/block] Once you have added all the [input](select-input-files) and reference files, you can [set your app's parameters](define-app-settings) and execute the task.