Preserving institutional knowledge

New guidance on using system R and R libraries

New R version updates I’ve written on the topic of R libraries before: Using system R installs Updating R libraries after updating With the latest update to R-4.3.1, we’ve had to change the install location and type, so we felt that an update post was in order. Let’s cover how to activate these new installs and how we are suggesting folks manage their R libraries going forward. New install locations New R installations will be managed using micromamba, which is a sort of extension and alternative implementation of a subset of conda commands and conda channels.

Submitting data to the NCBI Sequence Read Archive (SRA)

Submitting data to the NCBI Sequence Read Archive (SRA) Pre-processing steps Collect fastq.gz files for each sample Rename fastq.gz files from long name to short name per sample Get biosample data early (especially if it’s from collaborators) Links https://submit.ncbi.nlm.nih.gov/subs/sra https://www.ncbi.nlm.nih.gov/sra/docs/submitfiles Sample attributes page Biosample batch page Basic Checklist Project Title Public Description for Project Grant Funding Start a New Submission The example that I will provide is for a host-associated 16S sequencing study.


Introduction to MATLAB on the CQLS infrastructure Users that are looking to work with MathWorks MATLAB software are able to access it at the command line. First off, MATLAB will not run on the front end machines shell.cqls.oregonstate.edu and files.cqls.oregonstate.edu. Users are able to run the software stack on the processing machines using the -nodisplay option when accessing MATLAB via the command line. The CQLS has two versions R2022b and R2018a currently licensed for command line and batch usage as well as the MATLAB Distributed Computing Server (MDCS).

Guidance on using the CQLS queuing system

The CQLS queuing system Queuing systems allow for multiple users to make use of multiple compute nodes across an infrastructure. At the CQLS, we log in to the shell.cqls.oregonstate.edu machine, currently called vaughan. From vaughan, users can submit batch or array jobs (1 or many tasks, respectively) to the, queuing system such that they run autonomously, and will continue running even when users log off. Reading pre-requisite Please see this previous post with some information regarding the CQLS infrastructure along with some of the commands that are a part of the SGE queuing system.

Frequenty Asked Questions

New User ‘onboarding’ / FAQs Assumptions You have experience using the command-line; if not, see Training below Accounts How do I login? (SSH) When using mac or linux-based operating systems, you should have access to a terminal and the ssh program that will let you connect to the infrastructure. Using windows, you will need to use the Windows Subsystem for Linux (WSL) or putty. What server do I login to? You should log in to shell.

Using the system miniconda 3 install

Using the system miniconda 3 install I previously wrote about installing your own miniconda install here which I strongly suggest reading. However, after I received many questions about getting the conda set up properly, I decided to make the process of getting conda set up for you a bit easier. I wrote a script that will: Ensure you are not installing to your home directory. Eliminate the need to download the miniconda installer.