Stampede2 sra file download

 · When files are hosted online as direct downloads, you can use the wget (Web get) command to skip your local computer and download the file directly to TACC. Typically this makes use of the "Copy Link Address" option when you right click on a link in a web browser that would otherwise start a download to your computer.  · Stampede2's /home and /scratch file systems are mounted only on Stampede2, but the work file system mounted on Stampede2 is the Global Shared File System hosted on Stockyard. Stockyard is the same work file system that is currently available on Frontera, Lonestar5, and several other TACC resources. Once you are able to connect to Stampede2: do this IF your command interpreter (command shell) is csh or tcsh, and if you have a NEW Stampede2 account for class, copy a file of mine to bltadwin.ru file on Stampede2. Note this erases your bltadwin.ru file (not a problem if you have a new account).

I want to download all SRA file from the following project. Is there a method to download all the SRA files at the same time? rna-seq data-download. Share. Improve this question. Follow edited Oct 17 '17 at llrs. 4, 1 1 gold badge 13 13 silver badges 39 39 bronze badges. A member of the SRA submission staff pointed out that using. prefetch --type all SRR will download the original files. In this case, it means running the above within an EC2 instance colocated with the S3 bucket (so, us-east-1) and having installed and configured SRA Toolkit to work from AWS (as per this documentation). Unfortunately, the particular files I am concerned with are not. Download Configuration Archive: Download the configuration archive for the selected SRA. Upload Configuration Archive: Import a configuration for the selected SRA. Navigate to the directory where you saved the SRA configuration archive file and select it. The configuration files are distributed bltadwin.ru archives. Click Open.

What happens here is that for each SRA file that is first decompressed for paired-end file it is moved to a directory named SRA_File. More information about GNU parallel can be found here. On Stampede2, to run this kind of parallel jobs, we need to submit a job script to the system. The job script is below with some annotation. When files are hosted online as direct downloads, you can use the wget (Web get) command to skip your local computer and download the file directly to TACC. Typically this makes use of the "Copy Link Address" option when you right click on a link in a web browser that would otherwise start a download to your computer. Download metadata associated with SRA data From the search result page. SRA Run files do not contain any information about the metadata (sample information, etc.) linked to the data themselves. To download metadata for each Run in your Entrez query click Send to on the top of the page, check the File radiobutton, and select RunInfo in pull-down.