24 projects
tibanna
Tibanna runs portable pipelines (in CWL/WDL) on the AWS Cloud.
benchmark-4dn
Benchmark functions that returns total space, mem, cpu given input size and parameters for the CWL workflows
dcicutils
Utility package for interacting with the 4DN Data Portal and other 4DN resources
foursight
Serverless Chalice Application for Monitoring
dcicsnovault
Storage support for 4DN Data Portals.
smaht-submitr
Support for uploading file submissions to SMAHT.
foursight-cgap
Serverless Chalice Application for Monitoring
foursight-smaht
Serverless Chalice Application for Monitoring
foursight-core
Serverless Chalice Application for Monitoring
tibanna-ff
Tibanna runs portable pipelines (in CWL/WDL) on the AWS Cloud.
submit4dn
Utility package for submitting data to the 4DN Data Portal
dcicwrangling
Scripts and Jupyter notebooks for 4DN wrangling
magma-suite
Collection of tools to manage meta-workflows automation.
submit_cgap
Support for uploading file submissions to the Clinical Genomics Analysis Platform (CGAP).
dcicpyvcf
Variant Call Format (VCF) parser for Python
granite-suite
granite is a collection of software to call, filter and work with genomic variants.
encoded-core
Core data models for Park Lab ENCODE based projects
hic2cool
Converter between hic files (from juicer) and single-resolution or multi-resolution cool files (for cooler). Both hic and cool files describe Hi-C contact matrices. Intended to be lightweight, this can be used as an imported package or a stand-alone Python tool for command line conversion.
portal-pipeline-utils
Utilities for deploying pipelines and interfacing with portal infrastructure.
cgap-pipeline-utils
Collection of utilities for cgap-pipeline
subprocess-middleware-c4
Subprocess WSGI middleware and Pyramid tween.
bamsnap-cgap
A converter from .bam to .png for specific genomic region.
python-lambda-4dn
A forked version of python-lambda for 4DN-DCIC use in packaging and deploying lambda functions.
pypairix
Pypairix is a Python module for fast querying on a pairix-indexed bgzipped text file that contains a pair of genomic coordinates per line. For more information, see: https://github.com/4dn-dcic/pairix/blob/master/README.md.
