DNAnexus file bridge and tools

This is a simple webservice that allows fast retrieval of data object URIs for use in IGV etc. It also provides helpers to manage archival processes and perform cost audits.

run.py

Starts the DNAnexus file service whioch provides a simple HTTP interface to get files by sample and project. This is also the default application ran by the docker image.

Available API routes

All API routes only support GET requests. A token must be provided in the authentication header (Bearer XXXXXXXXX)

/whoami Returns the users identity based on the supplied authentication token.

/project Returns the project list

/project/<string:dx_project> Return the samples in a given project

/url/<string:dx_project>/<string:dx_file> Return the ephemeral URL for a given file in a project/sample.

dxarc.py

This API native helper functions to manage file archival. If performing archiving and/or renamin options ensure the script will have the expected effect by supplying the --dryrun option.

Example use cases

Archive all production TSO500 runs older than 3 months, excluding files that are also in 001_ToolsReferenceData

python dxarc.py --token XXXXXXX -f --project "^002(_.+TSO.*)$" --before 12w --visibility visible --notin "^001_Tool" --archive --rename "802\1"

• --token XXXX Provide a DNAnexus access token
• -f --project "^002_.+TSO" Find project matichin pattern of any name in project starting with 001_Tool
• --before 12w Only return projects created more than 12 weeks ago and files that have not been modified for 12 weeks
• --visibility hidden Only return files that are hidden
• --notin "^001_Tool" Excludes any files that ar also in any project matching the search regular expression
• --archive Archive found objects
• --rename "802$1" Renames projects with this pattern (used in conjunction with --project).

Unarchivng all files that are also in hidden 001_ToolsReferenceData

THis can be used to ensure any shared resources in 001 are live of they are also on any other project.

python dxarc.py --token XXXXXXX -f --object ".*" --type file --project "^001_Tool" --visibility hidden --follow --output reference_data.tsv --unarchive

• --token XXXX Provide a DNAnexus access token
• -f --objects '.*' --type file --project "^001_Tool" Find files of any name in project starting with 001_Tool
• --visibility hidden Only return files that are hidden
• --follow also return the same files in other projects
• --output reference_data.tsv Writes objects summarty to file (before any updates)
• --unarchive Unarchive found objects

Show storage and compute costs for all development projects and write analysis level compute cost audit

python dxarc.py --token XXXXXXX -f --project "^003_" --compute compute_audit.tsv

• --token XXXX Provide a DNAnexus access token
• -f --objects '.*' --type file --project "^001_Tool" Find files of any name in project starting with 001_Tool
• --compute compute_audit.tsv

The output from the compute cost audit can be visualised with the included R script compute_plot.R.

e.g. Rscript compute_plot.R compute_audit.tsv compute_audit.pdf

extract_vcf.py

DEVELOPMENT ONLY Extract VCF calls from DNAnexus.

extract_sanger.py

*** DEVELOPMENT ONLY *** Extracts Sanger results from directory containing results in excel format