Joel Armstrong's repositories
cactusSynteny
Using cactus graphs to find a synteny hierarchy (and, as a side effect, rough rearrangement breakpoints).
vertebrate-phylogeny
A phylogeny of vertebrates which have genome assemblies available
analysis-purgatory
Miscellaneous analyses that weren't/aren't expected to be part of a paper, but need source control anyway
aoc18
Advent of Code 2018
azureProvisioning
A small Ruby DSL to build and provision Azure images and VMs.
breaks
Search for breakpoints in query related to reference based on the gene order
cactusBenchmarks
Repo for running automated analyses on several benchmark regions, as a supplement to the Cactus unit tests.
cgcloud
Image and VM management for Jenkins, Spark and Mesos clusters in EC2
cPecan
C + python code for pairwise multiple sequence alignment, pulling out this functionality from the Cactus alignment program.
cwltest
Framework for testing CWL tools and workflows
foundationdb
FoundationDB - the open source, distributed, transactional key-value store
github-flavored-markdown-test
A reference for github-flavored-markdown styling (and possibly behavior)
kent
UCSC Genome Browser source tree. Stable branch: "beta".
mafTools
Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.
onlineCactusViz
Visualization of the online CAF algorithm
phast
PHAST
ragoutSimulations
Infrastructure for running Evolver simulations to test Ragout
syscall.rs
Raw system calls for Rust
toil
A scalable, efficient, cross-platform and easy-to-use workflow engine in pure Python
toil-vagrant
A vagrant setup to test Toil's interface to many different HPC systems
treeBuildingEvaluation
A set of scripts to evaluate the accuracy of gene trees in a HAL file