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arteria.yaml.example
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arteria.yaml.example
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---
hermes_base_url: http://130.238.178.239:9000/api/0.1
hermes_user: dummy_user
hermes_token: my_token
summary_host: testuppmax
summary_user: arteria
summary_host_key: /path/to/ssh/key
summary_destination: /tmp/summaries/
summary_ngi_pipeline_reports_destination: /tmp/summaries/ngi_reports
biotank_hosts: mm-xart002,mm-xart003
biotank_user: arteria
biotank_user_key: "/path/to/ssh/key"
check_cert_slack_channel: "#bottest"
remote_host: testuppmax
remote_user: arteria
remote_host_key: /path/to/ssh/key
remote_destination: /tmp/runfolders/
remote_sisyphus_location: /opt/arteria/arteria-siswrap-env/deps/sisyphus/sisyphus-latest
ngi_pipeline_url: https://irma1.uppmax.uu.se:4444/ngi_pipeline_upps
irma_api_key: aaaaaaaaaaaaaaaaaaaaaaaaaaaaa
irma_remote_path: ./staging/
irma_reports_remote_path: ./staging/reports/
irma_checksum_base_url: https://irma1.uppmax.uu.se:4444/arteria_checksum_staging/api/1.0
irma_siswrap_base_url: https://irma1.uppmax.uu.se:4444/arteria_siswrap_staging/api/1.0
delivery_service_url: http://some-host.com:9999/
irma_replace_expressions:
- 's/UPPNEX_PROJECT: a2009002/UPPNEX_PROJECT: ngi2016001/'
- 's/UPPNEX_QOS: seqver/#UPPNEX_QOS: seqver/'
send_mail_to: [email protected]
runfolder_service_port: 10800
bcl2fastq_service_port: 10900
siswrap_service_port: 10700
# The service URL polled in the runfolder sensor:
runfolder_svc_urls:
- http://testarteria1:10800/api/1.0/runfolders/pickup
incoming_svc_urls:
- url: http://testarteria1:10850/api/1.0/runfolders/next
dest_folder: /data/testarteria1/runfolders
remote_user: arteria
user_key: /home/arteria/.ssh/id_rsa
charon_api_token: dummy_token
charon_base_url: http://charon.url
slack_webhook_url: https://slack.webhook.url
charon_status_report_slack_channel: "#bottest"
delivery_workflow_status_slack_channel: '#bottest'
# String of file paths to exclude from the compressed archive (egrep syntax)
archive_excludes: "\"'^Config|^InterOp|^SampleSheet.csv|^Unaligned|^runParameters.xml|^RunInfo.xml\""
# Which file entries we should not link to when creating the archive copy of the runfolder
archive_exclude_links: "-e Data -e Thumbnail_Images"
# Number of fastq files to expect when creating archive. If we find less files than this
# then the action will fail.
archive_fastq_threshold: 10
archive_python_path: /opt/arteria/arteria-runfolder-env/bin/python
supr_api_user: apiuser
supr_api_key: apikey
supr_api_url: https://disposer.c3se.chalmers.se/supr-test/api