VirtualHood

Installation

Clone the VirtualHood repository using:

git clone https://github.com/AWGL/VirtualHood.git

For both CRM pipelines:

Requirements:

The required packages can be found in envs/VirtualHood

Additional requirements include:

• Runid
• Sampleid
• Worksheet number
• Referral-must be in variables file in the the form "referral="
• poly and artefacts list in /data/temp/artefacts_lists

For the old CRM pipeline:

source /home/transfer/miniconda3/bin/activate VirtualHood

python CRM_report.py <seqId> <sampleid> <worksheet> <referral> <NTC_folder_name>

source /home/transfer/miniconda3/bin/deactivate

For the new CRM pipeline:

source /home/transfer/miniconda3/bin/activate VirtualHood

python CRM_report_new_referrals.py <seqId> <sampleid> <worksheet> <referral> <NTC_folder_name>

source /home/transfer/miniconda3/bin/deactivate

For the panCancer pipeline:

Requirements:

The required packages can be found in envs/VirtualHood

Additional requirements include:

• poly and artefacts list in /data/temp/artefacts_lists

Required parameters:

• Runid
• Sampleid
• Worksheet number
• Referral- must be in variables file in the the form "referral="

Optional parameter:

• path - this must end with "/". If a path is not provided, the default ("/data/results/runid/RochePanCancer/") will be used.

source /home/transfer/miniconda3/bin/activate VirtualHood

python panCancer_report.py <seqId> <sampleid> <worksheet> <referral> <path>

source /home/transfer/miniconda3/bin/deactivate

Tests

To run unit tests: python -m unittest test_panCancer_report.py