Frequently asked questions (FAQ)
- How do I access the BioHPC Cloud workstations remotely?
Remote access documentation. See also a
description of a VNC connection on "Access"
page.
- 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), cbsulogin.biohpc.cornell.edu , 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 cbsulogin2.biohpc.cornell.edu and cbsulogin3.tc.cornell.edu.
You can also use Globus Online to transfer files, please see
Globus at BioHPC Cloud and Using Globus to Share Data for details.
- 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.
- 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.
- 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.
- 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
or
wget -O SavedFileName
"http://foo".
- 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).
- How do I install Perl modules without asking the system administrator?
Documentation for installing PERL modules locally.
- How do I connect my own SATA drive to the interactive workstations?
You can use drives formatted under Linux (with file systems such as ext2 or ext3),
and Windows (NTFS or FAT32). Follow these instructions.
If unsure, ask us for help.
- 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.
- 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.
- I would like all members of my lab to access each other home
directories.
See BioHPC group
access to home directories.