rupdecat, 4 months ago to hpc

Everything set up. Waiting for students.

First round of the #Snakemake for #HPC users course (in preparation).

#OpenScience and #Reproducibility do demand efforts! Teaching is important!

I am so excited. Like it's the first time in a classroom ... 😊

victorp, 10 months ago to python

5 Latest Tools You Should Be Using With Python for Data Science.
🗂️ The article provides insightful details on tools like ConnectorX, DuckDB, Optimus, Polars, and Snakemake which could enhance data wrangling, querying, manipulation, and workflow automation capabilities.

1. 🧰 ConnectorX: Simplifying the Loading of Data
2. 🧰 DuckDB: Empowering Analytical Query Workloads
3. 🧰 Optimus: Streamlining Data Manipulation
4. 🧰 Polars: Accelerating DataFrames
5. 🧰 Snakemake: Automating Data Science Workflows

https://www.makeuseof.com/latest-python-data-science-tools/

#Python #DataScience #ConnectorX #DuckDB #Optimus #Polars #Snakemake #Programming #DataAnalysis #Productivity

thatdnaguy, 11 months ago to bioinformatics

#Bioinformatics #HiveMind #SnakeMake #Docker

Uni cluster runs using Docker images, so I have snakemake setup to specify the images appropriately dispatching jobs.

But I'm switch back and forth between our Linux servers and the cluster. Aiming to run jobs on our servers using the same images to avoid version conflicts and unexpected behavior.

Anyone using snakemake with dockerhub images on a standard Linux server? The docs aren't clear on compatibility and how to set it up so far.

dfm, 1 year ago to random

As part of my https://show-your.work development, I've just released a new library for "staging out" computationally expensive (or otherwise inaccessible) rules in a https://snakemake.readthedocs.io workflow: https://github.com/dfm/snakemake-staging

If you use #snakemake, please check it out and let me know what you think!