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A number of additional tools and packages have been installed on all compute servers, as listed below. Note that some tools that have many sub-program binaries, or for which multiple versions are installed, are not available on the standard PATH. The /stor/system/opt directory on your system contains installation directories for these tools, which can be added to your PATH as needed.Some And some PODs also have additional software installed that is unique to that POD.
Installing software
Users can perform local (per-user) installations that do not require administrative (root/sudo) access. For software that does require sudo, or if you would like a package installed globally for use by others, please email us at rctf-support@utexas.edu.
Programs in /stor/system/opt
Some tool "suites" that have many sub-program binaries, are not made available on the standard PATH. The /stor/system/opt directory on your system contains installation directories for these tools, which can be added to your PATH as needed. Examples include multiple versions of the sratoolkit and the picard-tools suites.
Multiple software versions
Unlike TACC, we do not implement a module system. Rather, we install different versions of a program side-by-side, with names differing by their versions (for example:
- Rscript (the default version, same as Rscript-4-3.1), Rscript-4.3.1, Rscript-4.0.3, Rscript-3.6.3
- samtools (the default, version 1.10), samtools-1.9, samtools-1.11
In particular, multiple versions of R and Python are installed side-by-side. For more information, see:
Often you can see if there are multiple versions of a program installed just by typing its name and hitting the Tab key twice. For example, typing bedtools then Tab Tab shows this:
| Code Block |
|---|
bedtools bedtools-2.25.0 bedtools-2.26.0 bedtools-2.27.1 bedtools-2.28.0 |
Web-based application R Studio and Python JupyterHub software
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