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file_sources_conf.yml.j2
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file_sources_conf.yml.j2
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---
- type: dropbox
id: dropbox
label: Your Dropbox Files
doc: Your Dropbox files - configure an access token via the user preferences
accessToken: ${user.preferences['dropbox|access_token']}
- type: ftp
id: ebi-ftp
label: "EBI FTP server"
doc: "European Bioinformatic Institute FTP server"
host: "ftp.ebi.ac.uk"
user: "anonymous"
passwd: ""
timeout: 10
port: 21
- type: ftp
id: covid-monitoring
label: "SARS-CoV-2 result files"
doc: "SARS-CoV-2 variants and consensus sequences"
host: "xfer13.crg.eu"
user: "anonymous"
passwd: ""
timeout: 10
port: 21
- type: ftp
id: ncbi-ftp
label: "NCBI FTP server"
doc: "NCBI FTP server"
host: "ftp.ncbi.nlm.nih.gov"
user: "anonymous"
passwd: ""
timeout: 10
port: 21
- type: ftp
id: ensembl-ftp
label: "ENSEMBL FTP server"
doc: "ENSEMBL FTP server"
host: "ftp.ensemblgenomes.org/vol1/pub/"
user: "anonymous"
passwd: ""
timeout: 10
port: 21
- type: ssh
id: covid-crg-ftp-staging
requires_roles: covid-crg-ftp-staging-upload
writable: true
label: "CRG COVID data - staging"
doc: "Center for Genomic regulation COVID19 FTP server"
host: "xfer13.crg.eu"
user: "{{ covid_crg_ftp_staging_user }}"
passwd: "{{ covid_crg_ftp_staging_passwd }}"
timeout: 10
path: "/home/FTPvandenbeek/userspace/staging/"
config_path: ""
port: 2222
- type: s3fs
label: Genome Ark
id: genomeark
doc: Access to Genome Ark open data on AWS.
bucket: genomeark
anon: true
listings_expiry_time: 60
- type: s3fs
label: Paratus raw data
requires_groups: Paratus
id: paretus_raw
doc: Access to Paratus data on AWS.
bucket: paratus-collab/VGL/raw_data
writable: true
secret: "{{ paratus_aws_secret_access_key }}"
key: "{{ paratus_aws_access_key_id }}"
listings_expiry_time: 60
- type: s3fs
label: Paratus draft assemblies
requires_groups: Paratus
id: paretus_draft
doc: Access to Paratus data on AWS.
bucket: paratus-collab/VGL/draft_assemblies
writable: true
secret: "{{ paratus_aws_secret_access_key }}"
key: "{{ paratus_aws_access_key_id }}"
listings_expiry_time: 60
- type: s3fs
label: Genome Ark EXPORT HERE
requires_groups: GenomeArkExport
id: genomeark_galaxy
doc: Access to Genome Ark open data on AWS.
bucket: genomeark
writable: true
secret: "{{ genomeark_galaxy_aws_secret_access_key }}"
key: "{{ genomeark_galaxy_aws_access_key_id }}"
listings_expiry_time: 60
- type: s3fs
label: VGL genomeark-upload
requires_groups: GenomeArkExport
id: vgl_genomeark_upload
doc: Access to VGL Genome Ark data on AWS.
bucket: genomeark-upload/linelletest
writable: true
secret: "{{ genomeark_vgl_aws_secret_access_key }}"
key: "{{ genomeark_vgl_aws_access_key_id }}"
listings_expiry_time: 60
- type: s3fs
label: 1000 Genomes
id: 1000genomes
doc: Access to the 1000 Genomes Project with human genetic variation, including SNPs, structural variants, and their haplotype context.
bucket: 1000genomes
anon: true
listings_expiry_time: 60
- type: s3fs
label: The Cancer Genome Atlas
id: tcga-2-open
doc: Access to the Cancer Genome Atlas (TCGA)
bucket: tcga-2-open
anon: true
listings_expiry_time: 60
- type: s3fs
label: COVID-19 Data Lake
id: covid19-lake
doc: A centralized repository of up-to-date and curated datasets on or related to the spread and characteristics of the novel corona virus (SARS-CoV-2) and its associated illness, COVID-19
bucket: covid19-lake
anon: true
listings_expiry_time: 60
- type: s3fs
label: Encyclopedia of DNA Elements (ENCODE)
id: encode-public
doc: The Encyclopedia of DNA Elements (ENCODE) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI)
bucket: encode-public
anon: true
listings_expiry_time: 60
- type: s3fs
label: Coupled Model Intercomparison Project 6
id: esgf-world
doc: The sixth phase of global coupled ocean-atmosphere general circulation model ensemble
bucket: esgf-world
anon: true
listings_expiry_time: 60
- type: s3fs
label: CMIP6 GCMs downscaled using WRF
id: wrf-cmip6-noversioning
doc: High-resolution historical and future climate simulations from 1980-2100
bucket: wrf-cmip6-noversioning
anon: true
listings_expiry_time: 60
- type: s3fs
label: GBIF European region public datasets
id: gbif-open-data-eu-central-1
doc: The Global Biodiversity Information Facility is an international network and data infrastructure aimed at providing anyone, anywhere, open access to data about all types of life on Earth.
bucket: gbif-open-data-eu-central-1
anon: true
listings_expiry_time: 60
- type: s3fs
label: Element Biosciences
requires_groups: ElementBio
id: elembio-macro-galaxy
doc: Access to Element Biosciences data on AWS.
bucket: elembio-macro-galaxy
writable: false
secret: "{{ elementbio_aws_secret_access_key }}"
key: "{{ elementbio_aws_access_key_id }}"
listings_expiry_time: 60
- type: posix
id: gxy-archiver
label: GalaxyArchiver
doc: GalaxyArchiver Local Destination -- not for general use
root: "/corral4/{{ galaxy_instance_codename }}/archive/export/"
requires_roles: galaxy-archiver-role
writable: true