William Warriner

Cluster workflow feature to allow shell commands or script to run before remote server setup (e.g. slurm) (wrap install script)

117

I want to be able to connect to our institution's cluster using VS Code Remote SSH without the server running on a compute node instead of the login node. The...

Just as an FYI there is another curated list of this type of software: https://github.com/pditommaso/awesome-pipeline Theirs links back to this repository.

Rearrange Anaconda content on docs

3

Most information is here: https://docs.rc.uab.edu/workflow_solutions/using_anaconda Some information is here: https://docs.rc.uab.edu/cheaha/software/software/#anaconda-on-cheaha ## Collecting Cloud.rc specific information - [x] Move this: https://docs.rc.uab.edu/workflow_solutions/using_anaconda/#what-is-my-best-solution-for-installing-anaconda - [x] To here: https://docs.rc.uab.edu/uab_cloud/installing_software/#installing-software - [x] Note we have...

Documenting more S3 transfer utilities

11

## What would you like to see added? ### Caveat! Our understanding is that `s5cmd` uses `md5` hashes to verify binary content integrity during uploads only, not downloads. For more...

Continuous integration

2

Needs for CI: - [X] Checking validity of internal links without anchors (#240) - [ ] Checking validity of internal links with anchors - [ ] Checking validity of external...

Anaconda best practices for environment reproducibility

1

### What would you like to see added? Blog post describing good practice for mixing conda and pip: https://www.anaconda.com/blog/using-pip-in-a-conda-environment Also relevant: https://pythonspeed.com/articles/conda-dependency-management/

- [x] Account Management - [ ] Data Management - [x] .../Long Term Storage - [ ] .../Transfer - [x] Workflow Solutions - [x] Cheaha Guide - [x] .../Open OnDemand...

### What is inaccurate? The page at https://docs.rc.uab.edu/data_management/lts/interfaces/ assumes the user is using Cheaha, but does not mention this assumption. It is also not under the Cheaha Guide section. This...

Shared group resources - security and good practice

1

### What would you like to see added? Discuss security and good practice responsibilities of shared group resource owners in a central location. Periodic review of membership, permissions and access...

Update singularity documentation to account for migration from modules to node-local install of 4.1.2

2

### What is inaccurate? We are retiring old singularity versions as we roll out version 4.1.2. We will want to be sure to document the changes required for workflows. Old...