Course project: NAISS 2024/22-49
(contains resources on both Rackham and Dardel)
Magnetic reservation: naiss2024-22-49_1
from 09:00-14:00 CET today (reserved nodes will be used by default, no need to specify it in the Slurm job script)
Course project folder: /proj/introtouppmax/snakemake-hackathon
Dardel is down this week due to a major update. Feel free to use the resource next week and onwards.
You may use your prefered editor for the files.
Or:
VSCode with Rackham: http://docs.uppmax.uu.se/cluster_guides/vscode_on_rackham/
VDCodium on Bianca: http://docs.uppmax.uu.se/cluster_guides/vscodium_on_bianca/
Bianca is not included as a resource to the course project, you may use your own SUPR project if you wish to run on Bianca instead.
Environment we will be using during the hackathon:
If you wish to rebuild the snakemake environment created for the course, you may follow the steps below. Please change the /proj/introtouppmax/snakemake-hackathon
path to a different one.
You may of course tweak if you need additional/less packages for your workflows.
The files for the Snakemake scaling gexercise may be found in the folder /proj/introtouppmax/snakemake-hackathon/snakemake_scaling
.
Contents of snakemake_hq_uppmax.sh
(Slurm job example for Snakemake using HyperQueue):