web-based analysis tool for rare disease genomics
PLSQL JavaScript Python CSS HTML Perl Other
Clone or download
hanars Merge pull request #483 from macarthur-lab/fix-xbrowse-phenotips
Update xbrowse phenotips to create phenotips patients when needed
Latest commit 2393cd0 Jul 20, 2018
Permalink
Failed to load latest commit information.
breakpoint_search merged in breakpoint_search Feb 5, 2017
deploy fix typo Jul 10, 2018
docs Update custom_ref_pops.md May 25, 2017
reference_data removed unused file Jul 9, 2018
seqr Merge pull request #477 from macarthur-lab/misc_bug_fixes Jul 19, 2018
ui updated ui build Jul 20, 2018
xbrowse fix liftover import Jul 19, 2018
xbrowse_server update xbrowse phenotips to create phenotips patients when needed Jul 20, 2018
.gitignore pr feedback May 17, 2018
.travis.yml switch back to single install command. Otherwise travis.ci build hangs Jan 17, 2018
LICENSE.txt Initial commit - starting new repo in xbrowse organization Jan 7, 2014
README.md formatting Feb 28, 2018
add_case_review_indivs_to_existing_project.py updated gnomad ref. population slugs Oct 16, 2017
add_indivs_to_existing_project.py updated gnomad ref. population slugs Oct 16, 2017
add_new_project_by_chromosomes.py updated gnomad ref. population slugs Oct 16, 2017
add_new_project_directory.py add 'topmed' AFs by default Feb 14, 2018
add_new_project_from_ped_file.py add 'topmed' AFs by default Feb 14, 2018
add_new_project_from_vcf_and_ped.py add 'topmed' AFs by default Feb 14, 2018
add_new_project_from_vcf_and_xls.py add 'topmed' AFs by default Feb 14, 2018
add_new_project_from_xls_file.py add 'topmed' AFs by default Feb 14, 2018
collect_static.sh use python2.7 Jul 24, 2016
functional_tests_using_selenium.py renamed unit test files to *_tests.py Mar 12, 2017
install_dependencies.sh cd .. Jan 17, 2018
manage.py utility scripts for running the several commands neeeded to load a pr… Mar 23, 2015
requirements.txt updated anymail dependency Jul 13, 2018
run_postgres_database_backup.py added project Oct 24, 2017
servctl initial deployment code for redis May 16, 2018
settings fixed service hosts Sep 4, 2017
settings.py fixed REDIS_SERVICE_HOSTNAME env. var, added KIBANA settings Jul 19, 2018
setup.py removing residual xBrowse references Mar 31, 2017
shell.py added shortcut to 'VCFFile' Jul 13, 2018
wsgi.py Using DjangoWhiteNoise to fixed Django static file handling when DEBU… Mar 21, 2016

README.md

seqr

Build Status

seqr is a web-based analysis tool for rare disease genomics.

This repository contains the code that underlies the Broad seqr instance, as well as other seqr deployments.

Overview

seqr consists of the following components or micro-services:

  • seqr - the main client-server application - javascript + react.js on the client-side, python + django on the server-side.
  • postgres - SQL database used by seqr and phenotips to store project metadata and user-generated content such as variant notes, etc.
  • phenotips - 3rd-party web-based tool for entering structured phenotype information.
  • mongo - NoSQL database used to store variant callsets and reference data.
  • matchbox - a service that encapsulates communication with the Match Maker Exchange.
  • nginx - http server used as the main gateway between seqr and the internet.
  • elasticsearch - NoSQL database alternative to mongo that currently supports loading large callsets using a Spark-based hail pipeline.
  • kibana - (optional) dashboard and visual interface for elasticsearch.

Installation

Kubernetes-based Installation Instructions - The Kubernetes-based installation allows for fully scripted deployment of all seqr components. It supports local installation on any operating system using a virtualized environment (minikube) as well as cloud deployment on Google, AWS, and other clouds.

Manual Installation Instructions - walks through the steps to install all seqr components on MacOSX.

Data pre-processing and loading pipelines - hail pipelines for pre-processing and loading datasets into an elasticsearch datastore.

Please Note: seqr is still under active development, and undergoing refactoring. We suggest you contact us if you want to build on this repo.