...
| Code Block |
|---|
bedtools bedtools-2.25.0 bedtools-2.26.0 bedtools-2.27.1 bedtools-2.28.0 |
Programs and data 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.:
| Code Block | ||
|---|---|---|
| ||
export PATH="/stor/system/opt/sratoolkit.2.8.2-ubuntu64/bin:$PATH" |
/stor/system/opt also contains a directory with complete BLAST databases: /stor/system/opt/blastdb, which is updated regularly.
Programs and data in /mnt/bioi/tools
All compute servers have a shared, read-only /mnt/bioi directory mounted that contains many useful bioinformatics resources such as annotations and other references in /mnt/bioi/ref_genome and external data in /mnt/bio/data).
...
| Code Block | ||
|---|---|---|
| ||
export PATH="/mnt/bioi/tools/cellranger/8.0.0/bin":$PATH export PATH="/mnt/bioi/tools/UCSC_utils/2023_08:$PATH" |
Web-based
...
RStudio and
...
JupyterHub
...
applications
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.
| Software | Description | Access | Software | Help |
|---|---|---|---|---|
| JupyterHub Server | Python Notebook Server | Available on all compute servers https://<server_name>.ccbb.utexas.edu |
(e.g.
|
| Python 3.9 | About R and R Studio Server |
| RStudio Server | RStudio Web Interface |
...
| R 4.3.1 |
...
Standard OS Software
(to find in repo: frep -r pattern .| grep -v /spec/)
...