Download files in patric

Customizing a batch submission is nearly the same process as a default batch submission except that that it requires that you submit a special file declaring the steps of the custom pipeline that you wish to run. In order to do this, we use rast-process-genome-batch and we provide the workflow file document using the —workflow flag.

Please click the link below to look at the file that we are about to use. Please download this file by right clicking or control-clicking the link. We will name the file Workflow. Then save it to your current working directory. We may now submit our assembly job. We will use the --workspace-path-prefix parameter to shorten the library names that we are passing to the command:. Once the job is submitted we may use the p3-job-status command to determine if the job is queued, running, or completed:.

When the job is complete, we can browse the output of the job. The output files for the job are written to the workspace in a directory that is named as the output name for the job prefixed with a period:.

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Want more? Advanced embedding details, examples, and help! This will start the installation process. You should be able to take the defaults for all of the options. PCs running Ubuntu Linux version 14 or newer. PCs running Windows 7 or newer. The file download status will appear in the top right of the window; click on the download icon to view the status and to open the downloaded document: When the download is complete depending on your internet speed it may take several minutes since the disk image is megabytes in size , open the image by clicking on the downloaded file PATRIC You will know you need to do this if you doubleclick the PATRIC icon and see this dialog: If you see this, instead of doubleclicking the PATRIC icon, right-click it and select Open: If your user account has administrative privileges you will be prompted to allow the application to open.

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