Instructors:
Jason Macklin, Kurt Showmaker, Aaron McDivitt, Richard Yanicky, Lucie Hutchins, David McKenzie
Helpers:
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General Information
Singularity
is a container platform. It allows you to create and run
containers that package up pieces of software in a way
that is portable and reproducible. You can build a container
using Singularity on your laptop, and then run it on many
of the largest HPC clusters in the world, local university
or company clusters, a single server, in the cloud, or on a
workstation down the hall. Your container is a single file,
and you don’t have to worry about how to install all the
software you need on each different operating system.
Singularity is key to research reproducibility.
Who:
The course is aimed at graduate students and other researchers.
For IT security reasons this course is only open to JAX employees.
Where: This training will take place online.
The instructors will provide you with the information you will need to connect to this meeting.
Requirements:
Participants must bring a laptop with a
Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.).
They should have a few specific software packages installed (listed below).
Accessibility:
We are dedicated to providing a positive and accessible learning environment for all. Please
notify the instructors in advance of the workshop if you require any accommodations or if there is
anything we can do to make this workshop more accessible to you.
If your "HOME" environment variable is not set (or you don't know what this is):
Open command prompt (Open Start Menu then type cmd and press [Enter])
Type the following line into the command prompt window exactly as shown:
setx HOME "%USERPROFILE%"
Press [Enter], you should see SUCCESS: Specified value was saved.
Quit command prompt by typing exit then pressing [Enter]
The default shell in some versions of macOS is Bash, and
Bash is available in all versions, so no need to install anything.
You access Bash from the Terminal (found in
/Applications/Utilities).
See the Git installation video tutorial
for an example on how to open the Terminal.
You may want to keep Terminal in your dock for this workshop.
To see if your default shell is Bash type echo $SHELL in
Terminal and press the enter/return key. If the message printed does
not end with '/bash' then your default is something else and you can run
Bash by typing bash.
The default shell is usually Bash and there is usually no need to
install anything.
To see if your default shell is Bash type echo $SHELL in
a terminal and press the enter/return key. If the message printed does
not end with '/bash' then your default is something else and you can run
Bash by typing bash.