Page Comparison

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All POD compute servers have (nearly) identical Ubuntu 1820.04 Operating System configurations.

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 which that is unique to that POD.

Let us know if there is additional software you would like to have installed.

Web-based application R Studio and Python JupyterHub software

The following web application software is available on all PODs.  Accessing a POD node with your web browser will take you to an application login page where your BRCF account credentials can be used to access the application's web interface. Your default directory will be your Home directory. See Home directory quotas for important storage-quota related information. See also About R and R Studio Server and About Python and JupyterHub server help pages.

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Available on all compute servers

https://<server_name>.ccbb.utexas.edu
(e.g. https://gsafcomp01.ccbb.utexas.edu)

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The version of R used for R Studio Server is R 3.6.1 on most compute servers (R 3.6.3 after Winter 22-23 OS Upgrades). However R 4.0.3 is the R version on these compute servers:

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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. E.g.:

export PATH="/stor/system/opt/sratoolkit.2.8.2-ubuntu64/bin:$PATH"

Programs in /mnt/bioi/tools

All compute servers have a shared, read-only /mnt/bioi directory mounted that contains many useful bioinformatics resources such as annotations and other references in /mnt/bioi/ref_genome and external data in /mnt/bio/data).T

Specifically, the /mnt/bioi/tools directory contains several tool suites and their associated data (e.g. cellranger, GSEA), and each tool suite directory has multiple tool version sub-directories. Like the suites in /stor/system/opt, the associated binaries are not on your PATH by default, but can be added as needed, e.g.:

export PATH="/mnt/bioi/tools/cellranger/8.0.0/bin":$PATH
export PATH="/mnt/bioi/tools/UCSC_utils/2023_08:$PATH"

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:

• About R and R Studio Server
• About Python and JupyterHub server

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:

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

The following web application software is available on all PODs.  Accessing a POD node with your web browser will take you to an application login page where your BRCF account credentials can be used to access the application's web interface. Your default directory will be your Home directory. See Home directory quotas for important storage-quota related information. See also About R and R Studio Server and About Python and JupyterHub server help pages.

After the August 2023 maintenance, all POD compute servers now use R 4.3.1 as the R version in their RStudio Server web application. If your POD has multiple compute servers and you would like one to run a different R version, please contact us at rctf-support@utexas.edu.

Standard OS Software

(to find in repo: frep -r pattern .| grep -v /spec/)

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