{"metadata":{"image":[],"title":"","description":""},"api":{"url":"","auth":"required","results":{"codes":[]},"settings":"","params":[]},"next":{"description":"","pages":[]},"title":"Run a Data Cruncher analysis","type":"basic","slug":"run-an-analysis-using-data-cruncher","excerpt":"","body":"# Run an analysis\n\nData Cruncher allows you to enter and execute Python, R or Julia code to perform further analyses on your data on the CGC. This page will explain how you can access Data Cruncher from a project on the CGC, set up an analysis and execute code within the analysis. To run an analysis, you will need execute permissions in the project where the analysis is created.\n\n## Access Data Cruncher\n\nTo access Data Cruncher from your project, proceed as follows:\n1. Open the desired project on the CGC.\nThis project should contain the data that you want to analyze further using Data Cruncher.\n2. Click the **Interactive Analysis** tab.\n3. On the **Data Cruncher** card click **Open**.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/c99893e-run-an-analysis-using-data-cruncher-1.png\",\n        \"run-an-analysis-using-data-cruncher-1.png\",\n        245,\n        408,\n        \"#f3f6f7\"\n      ]\n    }\n  ]\n}\n[/block]\nThis will take you to the Data Cruncher home page. If you have previous analyses, they will be listed on this page.\n\n## Create an analysis\n1. In the top-right corner click **Create new analysis**. The **Create new analysis** wizard is displayed.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/c2452d5-run-an-analysis-using-data-cruncher-2.png\",\n        \"run-an-analysis-using-data-cruncher-2.png\",\n        556,\n        476,\n        \"#333\"\n      ]\n    }\n  ]\n}\n[/block]\n2. On the first screen, name your analysis in the **Analysis name** field.\n3. Select **JupyerLab** or **RStudio** as the analysis environment.\n4. Select the **Environment setup**. Each setup is a preinstalled set of libraries that is tailored for a specific purpose. [Learn more](doc:about-libraries-in-a-data-cruncher-analysis).\n5. Click **Next**.\n6. Select the instance for the analysis.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/246d84c-run-an-analysis-using-data-cruncher-3.png\",\n        \"run-an-analysis-using-data-cruncher-3.png\",\n        556,\n        476,\n        \"#e7eef1\"\n      ]\n    }\n  ]\n}\n[/block]\n\nThe **Instance type** list displays available instances along with their disk size, number of vCPUs and memory (shown in brackets). The default instance is **c5.2xlarge** that has **1024 GB** of EBS storage, **8 vCPUs** and **16 GB** of RAM. \n\n7. (Optional) Change [suspend time settings](#instance-inactivity).\n8. Click **Start the analysis**.\nThe CGC will start acquiring an adequate instance for your analysis, which may take a few minutes. \n\nAnalysis initialization goes through the following stages:\n\n* **Allocating the instance for your analysis** - Obtain an instance from the cloud infrastructure provider.\n* **Preparing the allocated instance**  - Load the required software onto the instance.\n* **Doing the final setup of the analysis environment** - Perform final settings and initialize the analysis environment.\nWhen the initialization process is completed, you will be automatically taken to the editor.\n\n<a name=\"instance-inactivity\"></a>\n\n## Suspend time\n\nSuspend time is the period of analysis inactivity after which the instance is stopped automatically. Inactivity implies that:\n\n* There is no keyboard or mouse activity in the editor.\n* No files have been modified or created in the analysis (in the `/sbgenomics/workspace` directory).\n\nApart from stopping the instance, this also includes stopping the analysis and saving all analysis files and output files. Besides the option to enable or disable suspend time for an analysis, you also can also adjust its duration. 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Run a Data Cruncher analysis


# Run an analysis Data Cruncher allows you to enter and execute Python, R or Julia code to perform further analyses on your data on the CGC. This page will explain how you can access Data Cruncher from a project on the CGC, set up an analysis and execute code within the analysis. To run an analysis, you will need execute permissions in the project where the analysis is created. ## Access Data Cruncher To access Data Cruncher from your project, proceed as follows: 1. Open the desired project on the CGC. This project should contain the data that you want to analyze further using Data Cruncher. 2. Click the **Interactive Analysis** tab. 3. On the **Data Cruncher** card click **Open**. [block:image] { "images": [ { "image": [ "https://files.readme.io/c99893e-run-an-analysis-using-data-cruncher-1.png", "run-an-analysis-using-data-cruncher-1.png", 245, 408, "#f3f6f7" ] } ] } [/block] This will take you to the Data Cruncher home page. If you have previous analyses, they will be listed on this page. ## Create an analysis 1. In the top-right corner click **Create new analysis**. The **Create new analysis** wizard is displayed. [block:image] { "images": [ { "image": [ "https://files.readme.io/c2452d5-run-an-analysis-using-data-cruncher-2.png", "run-an-analysis-using-data-cruncher-2.png", 556, 476, "#333" ] } ] } [/block] 2. On the first screen, name your analysis in the **Analysis name** field. 3. Select **JupyerLab** or **RStudio** as the analysis environment. 4. Select the **Environment setup**. Each setup is a preinstalled set of libraries that is tailored for a specific purpose. [Learn more](doc:about-libraries-in-a-data-cruncher-analysis). 5. Click **Next**. 6. Select the instance for the analysis. [block:image] { "images": [ { "image": [ "https://files.readme.io/246d84c-run-an-analysis-using-data-cruncher-3.png", "run-an-analysis-using-data-cruncher-3.png", 556, 476, "#e7eef1" ] } ] } [/block] The **Instance type** list displays available instances along with their disk size, number of vCPUs and memory (shown in brackets). The default instance is **c5.2xlarge** that has **1024 GB** of EBS storage, **8 vCPUs** and **16 GB** of RAM.  7. (Optional) Change [suspend time settings](#instance-inactivity). 8. Click **Start the analysis**. The CGC will start acquiring an adequate instance for your analysis, which may take a few minutes. Analysis initialization goes through the following stages: * **Allocating the instance for your analysis** - Obtain an instance from the cloud infrastructure provider. * **Preparing the allocated instance** - Load the required software onto the instance. * **Doing the final setup of the analysis environment** - Perform final settings and initialize the analysis environment. When the initialization process is completed, you will be automatically taken to the editor. <a name="instance-inactivity"></a> ## Suspend time Suspend time is the period of analysis inactivity after which the instance is stopped automatically. Inactivity implies that: * There is no keyboard or mouse activity in the editor. * No files have been modified or created in the analysis (in the `/sbgenomics/workspace` directory). Apart from stopping the instance, this also includes stopping the analysis and saving all analysis files and output files. Besides the option to enable or disable suspend time for an analysis, you also can also adjust its duration. Minimum suspend time is 15 minutes.