# Snakemake Hackathon

:::info
## Event info
**Hackathon date:** 22.05 , 10-16
**Location:** online
**Event page and registration:** https://ssl.eventilla.com/event/snakemake_hack (published on 21.3)
**Costs:** free of charge
**Max participants:** currently 25, to be updated if needed
**Collaborative document**: https://siili.rahtiapp.fi/snakemake_hack (draft)

:::

**Organizer:** CSC (Geoportti project)
**Collaborators:**
- projects: CodeRefinery, EuroCC2
- organizations: CSC, Aalto, ENCCS, PDC, UPPMAX ...?
- people:
- CSC: Antoni Golos, Laxmana Yetukuri, Samantha Wittke
- Aalto: Teemu Ruokolainen
- ENCCS: Yonglei Wang
- PDC (NAISS): Johan Hellsvik
- UPPMAX (NAISS): Diana Iusan
- **Registration** for all via CSC event page system

## Materials

- rendered: https://coderefinery.github.io/snakemake_hackathon/
- source: https://github.com/coderefinery/snakemake_hackathon

## Tentative schedule

All times Helsinki time (EEST)

9-10 Supercomputing concept refresher
10-11 Intro to Snakemake (AG)
11-12 Snakemake on HPC
12-13 Lunch break
13-15 Hackathon

## Participant stats

> Quick current counts: 

### Home organization nationality:

- UK:2
- Fin: 19
- Swe:10

### HPC experience:

- no: 1
- beginner: 20
- advanced: 10

### HPC access:

- Aalto Triton: 1
- CSC Mahti: 1
- CSC Puhti: 15
- LUMI: 2
- UPPPMAX: 7 (bianca, rackham/snowy)
- Other 5
- Oxford Arc: 2
- NAISS C3SE: 1
- VTT internal
- other (person from Lund)

### Snakefile:

- No: 18
- WIP: 6
- ready: 6
- Don't know: 1

## Planning meeting 4.4.24

- Idea and plan for the Hackathon
- morning: lectures, afternoon: hands-on

- HPC concepts; difference between clusters? (Dardel similar to LUMI)
- SLURM? :heavy_check_mark:
- "fair share"? job priorities
- about same
- conda
- some allow, some prefer containerized, CSC: tykky
- container
- singularity/apptainer
- local scratch

- Snakemake on your cluster?
- Do we want breakout rooms already here?
- CSC:
- doc: https://docs.csc.fi/apps/snakemake/
- tutorial: https://docs.csc.fi/support/tutorials/snakemake-puhti/
- own installation via "container wrapper": https://docs.csc.fi/computing/containers/tykky/
- LUMI:
- similar to CSC setup
- ...?
- Dardel
- same computer model as LUMI. Python and/or Snakemake configurations might differ
- UPPMAX
- Triton
- ENCCS

Have short intro for each cluster in beginning of hackathon session in breakoutrooms

- Example case for hackathon (people without own project)? Close to "real life" but not Science specific.
- fall back solution: word count from HPC carpentries
- add your example here:
- ..
- ..

- Involvement interest (all, add your initials)
- lectures
- LY
- AG
- hackathon
- DI
- YW
- JH
- advertising
- all

- Advertisement:
- CSC April training newsletter (SW) :heavy_check_mark:
- CSChpc twitter (SW) :heavy_check_mark:
- Geoportti (SW)
- EuroCC (YW)
- CodeRefinery (SW)
- TTT4HPC Day4 course (TR)
- Aalto SciComp (TR)
- NAISS :heavy_check_mark:
- ENCCS
-

## TODO

- ASAP:
- advertise (use list above)
- start material preparation (SW to coordinate CSC internal first, before opening for comnments/additions from others)
- Beginning of May:
- prepare environment / module on each system
- add cluster specific tabs to materials (all)
- prepare short cluster specific intros (all)
- Mid May:
- Course project (on each system)
- invite participants
- course resource reservation (on each system)

## Other existing related materials

- [CSC bio workflows with Nextflow course materials](https://a3s.fi/swift/v1/AUTH_53f5b0ae8e724b439a4cd16d1237015f/csc-training/workflows_workshop.html)
- [CSC workflows on HPC considerations - slides](https://a3s.fi/2001659-workflow-workshop/workflows.html#/)
- [CSC High Throughput Computing docs page](https://docs.csc.fi/computing/running/throughput/)
- [Uppsala snakemake BYOC](https://github.com/NBISweden/workshop-snakemake-byoc)
- [Snakemake tutorial](https://slides.com/johanneskoester/snakemake-tutorial)
- [CodeRefinery lesson](https://coderefinery.github.io/reproducible-research/workflow-management/)
- [Carpentries lesson](https://carpentries-incubator.github.io/workflows-snakemake/)
- [Snakemake workflows catalog](https://snakemake.github.io/snakemake-workflow-catalog/)
- [Snakemake video](https://www.youtube.com/watch?v=_dG9b3a9zkk&t=400s)
- [CSC Snakemake tutorial](https://docs.csc.fi/support/tutorials/snakemake-puhti/)
- [MultiXScale Workflows material](https://ocaisa.github.io/hpc-workflows/)
- [Universe HPC Snakemake lesson](https://github.com/UNIVERSE-HPC/course-material/tree/main/technology_and_tooling%2Fsnakemake)