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BioHPC Cloud:
: User Guide



Frequently asked questions (FAQ)


  1. How do I access the BioHPC Cloud workstations remotely?
    Remote access documentation. See also a description of a VNC connection on "Access" page.

  2. How do I transfer files between the lab workstations and my own computer?
    Use the free FileZilla or WinSCP software if you use a Windows PC (FileZilla documentation, FileZilla Wiki, WinSCP documentation). Use FileZilla if you are a Mac user (FileZilla documentation, FileZilla Wiki). Use scp or sftp if you are using Linux.
    There is a dedicated machine for login or file transfer only (only ssh/sftp, no VNC logins are accepted), , this machine can be used for file transfer to and from your home directory and it does not require reservation. This machine is also available from outside of Cornell. Backup file transfer machine is and
    You can also use Globus Online to transfer files, please see Globus at BioHPC Cloud and Using Globus to Share Data for details.

  3. How can I share files with other BioHPC Cloud users?
    If you don't mind all other users seeing your files, you can add read permission for all users on selected files and directories. If you need to share with only a group of users please contact us, and we can create an appropriate user group. For more information about Linux file  system permissions please refer to our "Linux for Biologists" workshops.

  4. How can I share files with external (non-BioHPC Cloud) users?
    You can request a temporary account for the collaborator and copy (or link) files to the temporary account home directory. The other way is to use Globus, please consult Using Globus to Share Data for details.

  5. My external collaborator (sequencing facility, etc) needs to transfer files to Cornell, how can I do it?
    For inbound data transfers you can request a temporary account for your external collaborator, you can grant access to your directory for this temporary account or we can move the data to appropriate user home directory. We have a standing agreement with Weill Cornell Genomics Resources Core Facility, you can ask them to transfer data to BioHPC Cloud storage and they will know how to proceed. Data from Cornell Genomics Facility can be transferred directly as it is an internal Cornell unit.

  6. How do I download files from the internet to the workstations?
    An easy way is to use the Firefox software. From the command line window, type the command "Firefox" then press "return". Make sure that your X-windows must be turned on before you can use Firefox (documentation). Another way is to use the wget tool. The command is
    wget http://foo

    wget -O SavedFileName "http://foo"

  7. How do I open PDF, Word, Excel, Powerpoint files on the Linux workstations?
    There are two options. You can either use FileZilla, WinSCP to transfer files to your own computer, or open the files directly using the GUI software on the Linux workstations. Check here for a list of Office software (documentation). In order to use these software, you need to start X-windows on your local computer (documentation).

  8. How do I install Perl modules without asking the system administrator?
    Documentation for installing PERL modules locally.

  9. I have started a command line program. How can I disconnect and still have the program running?
    Press CNTRL+Z to freeze the program, then type bg<ENTER> to put it in background mode. You can disconnect now and your program (in most cases) will continue running in the background, if you have a valid reservation on the workstation. Better way is to use screen, however it needs to be started before you run your program. For more information about how to use screen please check this assignment from our "Linux for Biologists" workshop.

  10. I need to install a program that requires administrator ("root") access. What can I do?
    You can ask us to install this program, we usually do it if the softare may be of general interest. You can use Docker to run install software in a container as an administrator, you can even use different Linux distribution (like Ubuntu). For details please refer to BioHPC Cloud Docker documentation.

  11. I would like all members of my lab to access each other home directories.
    See BioHPC group access to home directories.

  12. I would like to log in and transfer data between BioHPC machines over ssh without typing my password each time.
    Set up passwordless ssh access as follows:
    Log in to any BioHPC machine (e.g, one of the login nodes) and run the following commands:

    ssh-keygen -t rsa            # press enter a few times to skip over questions
    cat .ssh/ >> .ssh/authorized_keys  
    echo Host * >> .ssh/config
    echo StrictHostKeyChecking no >> .ssh/config

    chmod 700 .ssh
    chmod 600 .ssh/authorized_keys .ssh/config

  13. What to do if RStudio Server is sluggish or not responding.

    See tips of using RStudio.



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