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  1. #1

    Installing a command/program to a remote computer

    I downloaded a program called fastq-dump (for bioinformatics). While it does the job on my personal computer, it runs very slow.

    I have access to a remote computer that can get the job done faster. However, upon logging in, I realized that fastq-dump has not been installed there.

    Is there a possibility I can "transfer" the program from my computer to the remote computer?

  2. #2
    Linux Engineer docbop's Avatar
    Join Date
    Nov 2009
    Woodshed, CA
    Do you have an account on the other computer with sudo privileges you're going to need it to install an application. If you have the necessary privileges you should be able to ssh to the other computer and install your application the same way you did on your personal computer.
    A lion does not lose sleep, over the opinion of sheep.

  3. #3
    Linux Engineer drl's Avatar
    Join Date
    Apr 2006
    Saint Paul, MN, USA / CentOS, Debian, Slackware, {Free, Open, Net}BSD, Solaris

    A brief look at one source for the SRA toolkit suggests that the tools are written in C:
    The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format (Note that this is not required for submission). The Toolkit source code is provided in the form of the SRA SDK, and may be compiled with GCC. However, pre-built software executables are available for Linux, Windows, and Mac OS X ...
    The configuration tools are written in perl, java. Hence root, adminstrator access does not seem necessary:
    The Toolkit comes with a default configuration that will work for most users. You may elect to perform the following tests to confirm that your configuration is working correctly. The default location for the "download repository" is:

    * Linux: /home/[user_name]/ncbi/public
    * Mac OS X: /Users/[user_name]/ncbi/public
    * Windows: C:\Users\[user_name]\ncbi\public
    -- excerpt from Toolkit Documentation : Software : Sequence Read Archive : NCBI/NLM/NIH

    However, it appears that some work will be necessary to install and configure the toolkit.

    Best wishes ... cheers, drl
    Last edited by drl; 04-27-2014 at 07:19 PM.
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