https://github.com/biomarkersparkinson/pep-download
Science Score: 13.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (6.7%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: biomarkersParkinson
- License: apache-2.0
- Language: Shell
- Default Branch: main
- Size: 20.5 KB
Statistics
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
pep-download
To download from PEP, take the following steps:
- Get the PEP-services Docker image and convert it to a Singularity image. Detailed instructions are here.
- Configure things (below).
- Run the script (below).
Configure
Prepare the directories containing config and credentials
You should have received credentials and configuration files from the PEP team.
On your host machine, create a directory structure e.g. under ~/pepclient:
* Put the config files (ClientConfig.json, rootCA.cert and ShadowAdministration.pub) in a subdirectory named config.
* Put your OAuth token (JSON file) in a subdirectory named secrets and name it oauth.json.
* Create an empty subdirectory named ~/pepclient/working.
Make sure paths are correct
The download_column.sh expects the PEP client config and secrets to be at $HOME/pepclient, and the pep-services image to be at $HOME/pep-services.sif.
The auto_download.sh and download_column.sh scripts refer to a data directory to download the data to.
Columns.txt
Make sure the names of the columns you want to download are in columns.txt. They will be downloaded in order with one job per column.
Run the auto_download script
Run auto_download.sh periodically (e.g. with cron) to queue new download jobs.
Manual downloads
If you really want to, here are some manual download instructions.
Owner
- Name: Digital Biomarkers for Parkinson's disease
- Login: biomarkersParkinson
- Kind: organization
- Location: Netherlands
- Repositories: 1
- Profile: https://github.com/biomarkersParkinson