Shell scripts to download datasets for the Data2Services project.
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A project to automate the download of datasets for the data2services-pipeline using Shell scripts run in a Ubuntu Docker image.
docker pull vemonet/data2services-download
docker build -t vemonet/data2services-download .
This command will download files in /data/data2services.
docker run -it --rm -v /data/data2services:/data vemonet/data2services-download \
--download-datasets aeolus,pharmgkb,ctd \
--username my_login --password my_password \
--clean # to delete all files in /data/data2services
More datasets can be found in ./datasets
Shell scripts are executed to download each dataset. Add your own.
download.sh accordingly, you will find a lot of simple operations to download files already covered.$USERNAME and $PASSWORD variables if you need one.See the Wiki for more details on common Shell download operations.
Check in /datasets.
# XML
docker run -it --rm -v /data/data2services:/data vemonet/data2services-download --download-datasets clinicaltrials,pubmed,interpro,bioproject,clinvar,dailymed,dbsnp,flybase,orphanet,pdb
# TSV
docker run -it --rm -v /data/data2services:/data vemonet/data2services-download --download-datasets stitch,pharmgkb,drugcentral,bindingdb,ncbigene,ndc,stitch,genage,ncbigene,irefindex
# NCATS Translator program
docker run -it --rm -v /data/data2services:/data vemonet/data2services-download --download-datasets gote,disgenet,pathwaycommons,biogrid,wikipathways,preppi,clinicaltrials,pubmed,kegg
Content type
Image
Digest
Size
62.9 MB
Last updated
almost 7 years ago
docker pull vemonet/data2services-download