On the command line and in scripts, we use the Environment Module system to make software versions available in a modular and malleable way. Environment Modules provide modular access to one version of one or more software packages to help improve reproducibility. We use a system called EasyBuild to create modules for everyone to use - there are over a thousand modules already available. The modules listed here are the software modules available currently on the
gizmo compute cluster.
You can read more about how to use these modules and manage your compute environment on our Compute Environments page.
Custom Fred Hutch Modules
Scientific Computing maintains custom builds of R and Python.
The Fred Hutch modules have the prefix
fh. FH modules are specific to the Hutch and contain libraries that users have requested. The Fred Hutch modules inherit all
the libraries from EasyBuild base R and Python. The
fhR module contains many Bioconductor libraries.
We recommended using the
fh versions of R and Python since they
have many BioInformatics packages. Most software package requests are already satisfied with the
Specific information about which R Modules are available, including more information about R libraries can be found on our dedicated R Module page.
Specific information about which Python Modules and Bundles are available, including more information about packages installed in them can be found on our dedicated Python Module page.
Life Science/Bio Software Modules
Other software for life sciences that are available as modules can be found on our BioModules page. If you do not see the software you are looking for, email
scicomp to request it or add your own GitHub issue in the easybuild-life-sciences repo. Either way, please be specific about the source and version of the software you are interested in.
Updated: June 9, 2023Edit this Page via GitHub Comment by Filing an Issue Have Questions? Ask them here.