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Description:

aacrgenie 16.4.0

AACR Project GENIE

Introduction
This repository documents code used to gather, QC, standardize, and analyze data uploaded by institutes participating in AACR's Project GENIE (Genomics, Evidence, Neoplasia, Information, Exchange).
Documentation
For more information about the AACR genie repository, visit the GitHub Pages site.
Dependencies
This package contains both R, Python and cli tools. These are tools or packages you will need, to be able to reproduce these results:

Python >=3.8 or <3.10

pip install -r requirements.txt

bedtools
R 4.2.2

renv::install()
Follow instructions here to install synapser

Java > 8

For mac users, it seems to work better to run brew install java

wget

For mac users, have to run brew install wget

File Validator
One of the features of the aacrgenie package is that is provides a local validation tool that GENIE data contributors and install and use to validate their files locally prior to uploading to Synapse.
pip install aacrgenie
genie -v

This will install all the necessary components for you to run the validator locally on all of your files, including the Synapse client. Please view the help to see how to run to validator.
genie validate -h
genie validate data_clinical_supp_SAGE.txt SAGE

Contributing
Please view contributing guide to learn how to contribute to the GENIE package.
Sage Bionetworks Only
Developing locally
These are instructions on how you would develop and test the pipeline locally.

Make sure you have read through the GENIE Onboarding Docs and have access to all of the required repositories, resources and synapse projects for Main GENIE.

Be sure you are invited to the Synapse GENIE Admin team.

Make sure you are a Synapse certified user: Certified User - Synapse User Account Types

Clone this repo and install the package locally.
pip install -e .
pip install -r requirements.txt
pip install -r requirements-dev.txt

If you are having trouble with the above, try installing via pipenv

Specify a python version that is supported by this repo:
pipenv --python <python_version>

pipenv install from requirements file

Activate your pipenv:
pipenv shell

Configure the Synapse client to authenticate to Synapse.

Create a Synapse Personal Access token (PAT).
Add a ~/.synapseConfig file
[authentication]
authtoken = <PAT here>

OR set an environmental variable
export SYNAPSE_AUTH_TOKEN=<PAT here>

Confirm you can log in your terminal.
synapse login

Run the different pipelines on the test project. The --project_id syn7208886 points to the test project.

Validate all the files excluding vcf files:
python bin/input_to_database.py main --project_id syn7208886 --onlyValidate

Validate all the files:
python bin/input_to_database.py mutation --project_id syn7208886 --onlyValidate --genie_annotation_pkg ../annotation-tools

Process all the files aside from the mutation (maf, vcf) files. The mutation processing was split because it takes at least 2 days to process all the production mutation data. Ideally, there is a parameter to exclude or include file types to process/validate, but that is not implemented.
python bin/input_to_database.py main --project_id syn7208886 --deleteOld

Process the mutation data. Be sure to clone this repo: https://github.com/Sage-Bionetworks/annotation-tools and git checkout the version of the repo pinned to the Dockerfile. This repo houses the code that re-annotates the mutation data with genome nexus. The --createNewMafDatabase will create a new mutation tables in the test project. This flag is necessary for production data for two main reasons:

During processing of mutation data, the data is appended to the data, so without creating an empty table, there will be duplicated data uploaded.
By design, Synapse Tables were meant to be appended to. When a Synapse Tables is updated, it takes time to index the table and return results. This can cause problems for the pipeline when trying to query the mutation table. It is actually faster to create an entire new table than updating or deleting all rows and appending new rows when dealing with millions of rows.
If you run this more than once on the same day, you'll run into an issue with overwriting the narrow maf table as it already exists. Be sure to rename the current narrow maf database under Tables in the test synapse project and try again.

python bin/input_to_database.py mutation --project_id syn7208886 --deleteOld --genie_annotation_pkg ../annotation-tools --createNewMafDatabase

Create a consortium release. Be sure to add the --test parameter. Be sure to clone the cbioportal repo: https://github.com/cBioPortal/cbioportal and git checkout the version of the repo pinned to the Dockerfile
python bin/database_to_staging.py Jan-2017 ../cbioportal TEST --test

Create a public release. Be sure to add the --test parameter. Be sure to clone the cbioportal repo: https://github.com/cBioPortal/cbioportal and git checkout the version of the repo pinned to the Dockerfile
python bin/consortium_to_public.py Jan-2017 ../cbioportal TEST --test

Production
The production pipeline is run on Nextflow Tower and the Nextflow workflow is captured in nf-genie. It is wise to create an ec2 via the Sage Bionetworks service catalog to work with the production data, because there is limited PHI in GENIE.