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.biohpc.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.
- 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.
- 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:
cd
ssh-keygen -t
rsa
# press enter a few times to skip over questions
cat .ssh/id_rsa.pub >> .ssh/authorized_keys
echo 'Host *' >> .ssh/config
echo StrictHostKeyChecking no >> .ssh/config
chmod 700 .ssh
chmod 600 .ssh/authorized_keys .ssh/config
- What to do if RStudio Server is sluggish or not responding.
See tips for using RStudio.