Contents
Accessing Duke's Systems and Logging In
Web Page Access
Many of Babase's web pages are available to the public without restriction. However, those pages which access database content or allow data to be changed are restricted to those with Duke NetIDs. Before accessing these restricted pages, your Duke NetID and its password must be provided. On a future date, a second authentication check (a.k.a. multi-factor or two-step authentication) may also be required.
If you do not have a Duke NetID, contact the lab for sponsorship.
Be sure to have cookies turned on for all of the above.
Access to the Unix prompt with SSH
For most people the Babase web interface (phpPgAdmin) is all that's needed. More advanced users, particularly the data managers, require access to the Unix command prompt using SSH.
By default, SSH access is not available to everyone. You must explicitly be granted permission by the Duke data manager before you can SSH into the VM.
Be on Duke's network
To use SSH you must first be connected to Duke's network. Ways to do this:
- Be physically present at Duke
Set up the Duke VPN
SSH-ing in
(This will only work if you are on the Duke network)
From a Unix or Unix-like terminal (In macOS, use "Terminal". In Windows, you'll need to get some 3rd party software, but PuTTY is common), enter:
ssh MYDUKENETID@papio.biology.duke.edu
and hit enter. You will be asked for your NetID's password; when entering it, the cursor on the screen will not move, but rest assured that it is still accepting input. Hit enter to send the password, and you're in.
Transferring files to/from the VM with SCP
If you find a need to move files between your local computer and the VM, ideally you'd use SCP. Feel free to Google up an SCP tutorial of your choice, if you aren't already familiar with it. However, there's a problem that you should be aware of.
Duke's OIT requires the use of "user private groups". If you're unfamiliar with this idiom, again feel free to Google it. Usually, you should leave it enabled, but this keeps SCP commands from functioning. So you must temporarily disable it.
Disabling user private groups
There are lots of reasons why you might want to disable UPG. This is addressed here, related to SCP, because you need to disable UPG for SCP to work. If you have some other task that might be improved by disabling UPG, then you're likely an advanced-enough user that you know what you're doing and don't need this wiki to learn how.
After SSH-ing into the VM, enter:
emacs ~/.bashrc
A file will open, which will include the following text:
# Turn on the user-private-group idiom to collaborate with others. # See: https://security.ias.edu/how-and-why-user-private-groups-unix # THIS SHOULD ALWAYS COME AFTER THE SOURCING OF GLOBAL DEFINITIONS; # it effectively aborts and re-executes bash, but must not come before # the sourcing of global definitions because the global definitions # change the umask. # #echo 'Please consider editing ~/.bashrc and turning on collaboration' # If you do this, scp and remote ssh commands BREAK. But if you don't # anything you create, with scp or otherwise, will be editable only by # you. The recommended approach is to turn UPG collaboration off # whenever you scp, then scp into your home directory, then turn UPG # back on and ssh in again and copy the data into the desired location # for collaboration. # # To turn collaboration on, uncomment the line below and comment # the "echo" above. source /usr/local/bin/upg_enable
In this case, UPG--or "collaboration", as described above--is already enabled. To turn it off, add a "#" to the beginning of the "source" line. Normally, you'd also want to remove the "#" from the beginning of the "echo" line; removing that "#" ensures that you get a text alert that UPG is turned off. However, this text alert also breaks SCP.
So, to disable UPG to allow SCP:
- Comment out both the "echo" and "source" lines with "#"
- Save these changes by entering Ctrl-X, Ctrl-S
- Leave emacs by entering Ctrl-X, Ctrl-C
You will need to logout of Papio and back in if you want this UPG change to take effect in any already-active connection(s) you may have to the VM.