iscan_to_dnanexus

Upload data from local server to DNAnexus

What does this tool do?

Identifies iScan data stored on local server an uploads to specific DNAnexus project using upload agent

What are typical use cases for this tool?

Usually run once a week by Duty Bioinformatician to push new iScan data to DNAnexus

What data are required for this app to run?

iScan data and api token must be available (with appropriate permissions) on the local server

What does this tool output?

Output/error logs from upload agent

NOTE TO DEVELOPERS

Please don't commit config files to this repo. We've left it out of .gitignore as we don't restrict what you can name the config file, and as such can't catch every possibility, so be mindful you don't accidentally commit config data to your branch.

Instructions

Setting the config file

A config file must be written before invoking the script. The file can have any name, but must be written as follows:

AUTH_TOKEN_PATH=
ISCAN_DIR=
UPLOAD_AGENT_PATH=
DX_PROJECT_ID=
ARCHIVE_DIR=

The config fields are defined as follows:

• AUTH_TOKEN_PATH: path to a file containing your DNANexus API token
• ISCAN_DIR: path to parent folder containing iScan output data
• UPLOAD_AGENT_PATH: path to DNANexus Upload Agent executable (see https://documentation.dnanexus.com/downloads#upload-agent)
• DX_PROJECT_ID: Target DNANexus project identifier
• ARCHIVE_DIR: path to a folder where files will be moved after upload. The subdirectory file structure remains the same for each dataset moved to archive.

See iscan_upload.conf.example for a template.

Exporting the config file

The file must then be stored as a bash variable with export - run the following before executing the script:

export ISCAN_CONFIG_PATH=/path/to/your_config.conf

Running the script

Run the following:

bash iscan_upload.sh

The script will parse the config file stored in ISCAN_CONFIG_PATH, and begin uploading your data to DNANexus.

Troubleshooting

iscan_upload.sh: line 20: $ISCAN_CONFIG_PATH: ambiguous redirect

This means you didn't define or export ISCAN_CONFIG_PATH, or the path you entered doesn't point to an existing file.