Hurwitz Lab's repositories
singularity-patric-cli
A singularity image for patric-cli https://docs.patricbrc.org/cli_tutorial/index.html
launch-yourself
Template script and instructions for using the TACC Launcher on Stampede.
singularity-graftM
Singularity image of https://github.com/geronimp/graftM
VirSorter-Euk
Source code of the VirSorter App, available on CyVerse (https://de.iplantcollaborative.org/de/)
saffrontree
Stampede2 SaffronTree
mash-on-patric
Running mash on patric to collapse strains into tighter species groupings
tacc-launcher-example
Example of using the TACC Launcher
karect
Karect for Stampede2
isogenie-assemblies
Isogenie assembly work
isogenie-permafrost
Isogenie work on permafrost scripts
dfu-bubble-plots
Repo to generate some figures for the DFU project
virsorter-singularity
Singularity container for VirSorter to run on stampede2
robotframework-jsonlibrary
Robotframework Test Library to manipulate JSON using JSONPath
interpro
Singularity/Stampede2 InterPro
pave
PaVE
refseq-mash
MinHash RefSeq for species discovery
download-tcga
Scripts to download / manipulate TCGA data from GDC (or EBI data in one case)
agave-file-browser
Agave File Browser
infant_diabetes
Pipeline for analysis of "A prospective, longitudinal analysis of the developing gut microbiome in infants en route to type 1 diabetes"
d3.chart.bubble-matrix
A bubble-matrix chart based on d3.chart
mds.js
Classic Multidimensional scaling code in Javascript
singularity-python-faves
Scott's favorite pythonic bioinformatic tools / scripts (and possible a few others :) )
download-dbgap
Just simple script(s) to download SRA data from dbgap
ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
patric-curation
A pipeline to curate the PATRIC database for phages and other necessary tasks
stampede-fizkin
Fizkin/Singularity for TACC/stampede