uc-cwr
The code base for the Crop-Wild-Relative (CWR) Biodiversity Digital Twin use-case led by UiO
Science Score: 49.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 5 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (7.4%) to scientific vocabulary
Repository
The code base for the Crop-Wild-Relative (CWR) Biodiversity Digital Twin use-case led by UiO
Basic Info
Statistics
- Stars: 2
- Watchers: 2
- Forks: 4
- Open Issues: 9
- Releases: 3
Metadata Files
README.md
uc-CWR
Initial setup
- Create a file
R_scripts/SHARED-APICredentials.R. You can use the example file as a template. Insert your CDS API key and GBIF credentials in this file.
ModGP on Rstudio
- Source
ModGP_MASTER.Rand changeSPECIESargument at line 19 to execute ModGP pipeline for a specific genus.
ModGP on LUMI with Hyperqueue
Install HyperQueue:
wget https://github.com/It4innovations/hyperqueue/releases/download/v0.18.0/hq-v0.18.0-linux-x64.tar.gz tar -xvf hq-v0.18.0-linux-x64.tar.gz rm hq-v0.18.0-linux-x64.tar.gz
Fetch the container:
singularity pull --disable-cache docker://ghcr.io/biodt/cwr:0.5.3
Submit calculation job for a desired species (e.g. Lathyrus):
sbatch submitmodgppreplumi.sh Lathyrus sbatch submitmodgpexeclumi_HQ.sh Lathyrus
CAPFITOGEN demo
See documentation.
Download
CAPFITOGEN3.zipfrom here and extract it to the project root.Download
rdatamaps/world/20x20directory from here and extract it toCAPFITOGEN3/rdatamaps/world/20x20.Run on LUMI: obtain interactive session:
srun -p small --nodes=1 --ntasks-per-node=1 --mem=8G -t 4:00:00 --pty bashand execute the workflow:singularity run --bind $PWD cwr_0.2.0.sif capfitogen.R
Related publication
Chala D, Kusch E, Weiland C, Andrew C, Grieb J, Rossi T, Martinovic T, Endresen D (2024) Prototype biodiversity digital twin: crop wild relatives genetic resources for food security. Research Ideas and Outcomes 10: e125192. https://doi.org/10.3897/rio.10.e125192
Archived at Zenodo
Owner
- Name: BioDT
- Login: BioDT
- Kind: organization
- Website: https://biodt.eu
- Twitter: BiodiversityDT
- Repositories: 1
- Profile: https://github.com/BioDT
Horizon EU Biodiversity Digital Twin
GitHub Events
Total
- Create event: 13
- Release event: 1
- Issues event: 24
- Watch event: 1
- Delete event: 1
- Issue comment event: 72
- Member event: 2
- Push event: 77
- Pull request event: 36
- Pull request review event: 11
- Fork event: 3
Last Year
- Create event: 13
- Release event: 1
- Issues event: 24
- Watch event: 1
- Delete event: 1
- Issue comment event: 72
- Member event: 2
- Push event: 77
- Pull request event: 36
- Pull request review event: 11
- Fork event: 3
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 13
- Total pull requests: 20
- Average time to close issues: 2 days
- Average time to close pull requests: 8 days
- Total issue authors: 3
- Total pull request authors: 5
- Average comments per issue: 1.85
- Average comments per pull request: 0.95
- Merged pull requests: 13
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 13
- Pull requests: 20
- Average time to close issues: 2 days
- Average time to close pull requests: 8 days
- Issue authors: 3
- Pull request authors: 5
- Average comments per issue: 1.85
- Average comments per pull request: 0.95
- Merged pull requests: 13
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- evalieungh (5)
- MichalTorma (5)
- trossi (3)
- dnlbauer (1)
Pull Request Authors
- evalieungh (6)
- trossi (5)
- dagendresen (5)
- MichalTorma (3)
- saanavainiocsc (2)
- dnlbauer (1)
- helijuottonen (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- base latest build
- docker.io/opensuse/leap 15.4 build