The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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The CyVerse App Store is currently being restructured, and apps are being moved to an HPC environment. During this transition, users may occasionally be unable to locate or use apps that are listed in our tutorials. In many cases, these apps can be located by searching them using the search bar at the top of the Apps window in the DE. To increase the chance for search success, try not searching the entire app name and version number but only the portion that refers to the app's function or origin (e.g., 'SOAPdenovo' instead of 'SOAPdenovo-Trans 1.01').

Also, as part of the 2.8 app categorization, a number of apps were deprecated and are no longer available, and there is no longer an Archive category. You can search for a suitable replacement in the List of Applications in this window, or search on an app name or tool used for an app in the Apps window search field. If you need an app reinstated, please contact support@cyverse.org.

In critical cases, please report your concern to the CyVerse Ask forum or to support@cyverse.org. Thank you for your patience.

The DE Quick Start tutorial provides an introduction to basic DE functionality and navigation.

Please work through the tutorial and add your comments on the bottom of this page, or send comments per email to upendra@cyverse.org. Thank you.

Rationale and background: 

curl is a tool to transfer data from or to a server, using one of the supported protocols (DICT, FILE, FTP, FTPS, GOPHER, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMB, SMBS, SMTP, SMTPS, TELNET and TFTP). The command is designed to work without user interaction.

curl offers a busload of useful tricks like proxy support, user authentication, FTP upload, HTTP post, SSL connections, cookies, file transfer resume, Metalink, and more. As you will see below, the number of features will make your head spin!

curl is powered by libcurl for all transfer-related features. See libcurl(3) for details


Prerequisites

  1. A CyVerse account. (Register for an CyVerse account here - user.cyverse.org.)

  2. Input

    1. URL: The URL syntax is protocol-dependent
  3. Output
    1. Output File Name: Write output to <file> instead of stdout
  4. Parameters
    1. insecure: This option allows curl to proceed and operate even for server connections otherwise considered insecure. The server connection is verified by making sure the server's certificate contains the right name and verifies successfully using the cert store.

Test/sample data:

Use the following inputs/outputs and parameters for testing curl-7.45.0

  1. Input

    1. URL: ftp://ftp.ncbi.nih.gov/refseq/M_musculus/mRNA_Prot/mouse.1.protein.faa.gz

  2. Output

    1. Output File Name: mouse.1.protein.faa.gz
  3. Optional arguments/parameters: None


More information about Scythe-0.991 can be found at curl

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