Package: aacrgenie
AACR Project GENIEIntroductionThis 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).DependenciesThis 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 <3.10pip install -r requirements.txtbedtoolsR 4.2.2renv::install()Follow instructionshereto install synapserJava > 8For mac users, it seems to work better to runbrew install javawgetFor mac users, have to runbrew install wgetFile ValidatorOne of the features of theaacrgeniepackage 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 -vThis 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 SAGEContributingPlease viewcontributing guideto learn how to contribute to the GENIE package.Sage Bionetworks OnlyDeveloping locallyThese are instructions on how you would develop and test the pipeline locally.Make sure you have read through theGENIE Onboarding Docsand 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 TypesClone this repo and install the package locally.pip install -e .
pip install -r requirements.txt
pip install -r requirements-dev.txtIf you are having trouble with the above, try installing viapipenvSpecify a python version that is supported by this repo:pipenv --python <python_version>pipenv install from requirements fileActivate yourpipenv:pipenv shellConfigure the Synapse client to authenticate to Synapse.Create a SynapsePersonal Access token (PAT).Add a~/.synapseConfigfile[authentication]
authtoken = <PAT here>OR set an environmental variableexport SYNAPSE_AUTH_TOKEN=<PAT here>Confirm you can log in your terminal.synapseloginRun the different pipelines on the test project.  The--project_id syn7208886points to the test project.Validate all the filesexcluding vcf files:python bin/input_to_database.py main --project_id syn7208886 --onlyValidateValidateallthe files:python bin/input_to_database.py mutation --project_id syn7208886 --onlyValidate --genie_annotation_pkg ../annotation-toolsProcess 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 --deleteOldProcess the mutation data.  Be sure to clone this repo:https://github.com/Sage-Bionetworks/annotation-toolsandgit checkoutthe version of the repo pinned to theDockerfile.  This repo houses the code that re-annotates the mutation data with genome nexus.  The--createNewMafDatabasewill 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 underTablesin the test synapse project and try again.python bin/input_to_database.py mutation --project_id syn7208886 --deleteOld --genie_annotation_pkg ../annotation-tools --createNewMafDatabaseCreate a consortium release.  Be sure to add the--testparameter. Be sure to clone the cbioportal repo:https://github.com/cBioPortal/cbioportalandgit checkoutthe version of the repo pinned to theDockerfilepython bin/database_to_staging.py Jan-2017 ../cbioportal TEST --testCreate a public release.  Be sure to add the--testparameter.  Be sure to clone the cbioportal repo:https://github.com/cBioPortal/cbioportalandgit checkoutthe version of the repo pinned to theDockerfilepython bin/consortium_to_public.py Jan-2017 ../cbioportal TEST --testProductionThe production pipeline is run on Nextflow Tower and the Nextflow workflow is captured innf-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.