In addition to the core software tools that are available by default, additional software is available via different Software Repositories. Note that some of these software tools are installed and maintained by other users or research groups of the cluster who have kindly agreed on sharing their efforts with other cluster users. Currently known and publicly shared repositories are:
| Repository | Description |
|---|---|
|
CBC |
The Computational Biology and Informatics (CBI - formerly CBC) Software Repository Repository of software shared by Computational Biology and Informatics (http://cbi.ucsf.edu) at the UCSF Helen Diller Family Comprehensive Cancer Center. See the Software Repositories page for further details. |
To get access to the software available in one or more of these repositories, load the repository using module load <repos> (on command line and in script). After loading a software repository, all of its software tools are available as environment modules, that is, they can in turn be loaded using module load <software>.
The R software is available in software repository CBC. To use that R installation, first make sure to enable (“load”) the repository and then the software as in:
module load CBC ## Enables the software repository
module load r ## Enables R
or, shorter (order is important):
module load CBC r
After this, the R (and the Rscript) commands are available on the search path (PATH), e.g.
$ Rscript --version
R scripting front-end version 3.4.1 (2017-06-30)
To disable (“unload”) R, that is, remove it from the search path, do:
module unload r
To see what software modules you have currently loaded, use:
module list
To disable all loaded software modules and repositories, use:
`module purge
To see what software modules are currently available (in the software repositories you have loaded), use:
module avail
or alternative,
module spider
If the software repository provides more than one version of each software, specific versions can be loaded using the module load <software>/<version> format. For instance, the CBC repository provides a large number of historical R versions. To load R 3.1.3, use:
module load r/3.1.3
Comment: If another version of R is already loaded, that will automatically be unloaded before loading the new version.
CBC) whereas the names of the software themselves are always in lower case (e.g. r and bwa). This makes it easier to distiguish between repositories and software.
For more information on how to use modules and the module command, see module --help, man module, and the official Lmod documentation.
Instead of the classical Tcl-based environment module system commonly available on Linux, Wynton uses a Lua-based environment module system called Lmod. Lmod has a several advantages over the Tcl-based module system while being backward compatible, i.e. users of Tcl modules can still use them with Lmod. There are a few rare corner cases where a Tcl module might fail and the module has to be rewritten as a Lua-based module.
When loading a software repository (module load <repos>), it will append its module folder to the $MODULEPATH. Unloading it (module unload <repos>) will undo any changes. For instance, module load <repos> appends $MODULEPATH_ROOT/<repos> to your $MODULEPATH. Multiple software repositories can be loaded in one call, e.g. module load <repos1> <repos2>. It is also possible to load a software repository and some of its software tools in one call, e.g. module load <repos> <software1> <software2>.