Content Comparison

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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

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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

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="/mntstor/bioisystem/tools/cellranger/8.0.0/bin":$PATH
export PATH="opt/sratoolkit.2.8.2-ubuntu64/bin:$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/

...

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:

...

ref_genome and external data in /mnt/bio/data).

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"

Web-based application R Studio and Python JupyterHub software

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