Sharing files with us.

There are currently five ways to share your files with us:

  1. Use our data submission forms;
  2. Transmit the file via ftp (recommended only for files < 2 Gb);
  3. Email it to us (for files < 25 Mb only);
  4. Provide us with a URL, if available;
  5. Upload the file to CyVerse and share with our organization, NAL Bioinformatics.

We prefer that you share your files with us via our data submission forms. For instructions on how to use the forms, please see our data submission overview.

If you are unable to share your files with us via the data submission forms, you may use one of the other four methods. Here, we list the requirements for each method:

1. Ftp

  • Complete the relevant dataset submission form. After submitting it, we will send you an email with our ftp site information (Note that this information changes frequently).
  • To upload your file:

    • Navigate to the directory where your file resides.
    • From the command line, type ftp i5k_nal@ftp.nal.usda.gov, and enter the password when prompted.
    • If you are using a standalone or browser-based ftp client, connect to ftp.nal.usda.gov and log in using i5k_nal as the user, along with the provided password.
    • Make a directory for your data (e.g. mkdir genus_species_date) and navigate to that directory (cd genus_species_date)
    • load your data into this directory (e.g. put myfile.fa)
    • log out (e.g. bye)
  • Email i5k@ars.usda.gov informing us that you have transferred your file to our ftp server. Include in this email:

    • The organism name;
    • The file name;
    • The file md5sum
  • We will let you know whether the file transferred correctly, usually within 2 business days.

Note: If you are having problems transferring files to us via ftp, you may need to enable passive mode transfer.  Many modern ftp clients support passive mode by default, but command line interface ftp clients may need to be set to enable passive mode. Please refer to your ftp program documentation for more information.
Additional reading:
http://slacksite.com/other/ftp.html
http://www.serv-u.com/kb/1138/active-and-passive-ftp-transfers-defined

2. Email

  • Once you have completed the relevant dataset submission form, email i5k@ars.usda.gov with the following information:

    • The organism name;
    • The file name;
    • The file md5sum;
    • The attached file.
  • We will let you know whether we received the file, usually within 2 business days.

3. URL

  • If the file is available via URL (e.g. from the NCBI ftp site), once you have completed the relevant dataset submission form, email i5k@ars.usda.gov with the following information:

    • The organism name;
    • The file name;
    • The file URL (preferably to the file itself, not a parent directory).
  • We will let you know whether we could download the file, usually within 2 business days.

4. CyVerse

  • Once you have completed the relevant dataset submission form, share the file with us via CyVerse (Instructions are here).
  • Send an email to i5k@ars.usda.gov with the following information:

    • The organism name;
    • The path(s) to the shared file(s) on CyVerse (e.g. /username/my_analysis/alignment.bam)