CD2H gitForager

Fred Hutchinson Cancer Research Center

Login: FredHutch

Company: null

Location: Seattle

email:

Blog: http://fredhutch.org

Members

Repositories

ad2openldap: Replicate user, group, nis information from a Microsoft Active Directory server into an OpenLDAP server
atombaby-slurm-drmaa: null
au-slurm-package: The various configs and tools we use on the GenomeDK cluster
automatic-garbanzo: Repository containing Jenkins file for build automation
aws-batch-at-hutch-docs: null
aws-batch-helpers: Helper scripts to run and monitor jobs on AWS Batch
aws-batch-wrapper: Simplify interaction with AWS Batch at Fred Hutch
batch-dashboard: null
batch-demo: null
batch-event-writer: lambda function to write AWS Batch job state transition events to MongoDB
batch_instance_tagger: Does what Batch does not always do (tag instances with compute environment tags)
batchit: simple jobs submission via command-line for AWS batch
batch-pi: Calculate PI using Monte Carlo simulation and AWS Batch Processing
batch_pipeline: Example workflows for a multi-step array job on AWS Batch
batch-wrapper-client-golang: golang wrapper client is easier to deploy
beegfs-chunk-parity: This is a raid-5 addon for the beegfs storage system. Not ready for production yet.
chef-herman: null
chromium-zfs-beegfs: Full configuration of FredHutch Scratch File System using commodity disks, Ubuntu ZFS and BeeGFS
citest: repo for tetsing CI
cookbook-beagle-cluster: Role/Application cookbook for Beagle cluster resources
cookbook-objectivefs: A cookbook for managing ObjectiveFS mounts
cookbook-slurm-wlm: Chef Cookbook for Slurm
curly-guacamole: An introduction to the Chef workflow used by Scientific Computing
CutAndRun-Seq: Analysis tools and gh-pages for CutAndRun-Seq technology
dask-drmaa: Deploy Dask on DRMAA clusters
DataSpaceR: An R package for CAVD DataSpace
DataSpaceR.test: null
DB4SCI: Containerized Database Service (DBaaS)
dmtcp: DMTCP: Distributed MultiThreaded CheckPointing
docker-bwa: Docker image running BWA
docker-castor: Docker image running castor
docker-diamond: Docker image running DIAMOND
docker-eggnog-mapper: Docker image for eggNOG mapper
docker-fredhutch-ubuntu: Freeze official ubuntu docker image for reproducibility.
docker-humann2: Docker image running HUMANN2
docker-ls2: Basic Ubuntu-based docker container for batch use.
docker-metaphlan: Docker image running MetaPhlAn
docker-metaspades: Docker image running metaSPAdes
docker-midas: Docker image running MIDAS
docker-mocat: Docker image running MOCAT2
docker-mothur: Docker image running MOTHUR
docker-sciluigi-tools: Lightweight Docker image running Prokka
docker-sra: Get data from SRA
docker-swarm: Docker image running Swarm
docker-virfinder: Docker image running VirFinder
docker-vsearch: Docker image running VSEARCH
dotnet_demo: ASP.NET Demo
drat: Drat Repository for R Packages from Fred Hutch
dts-linux-toolkit: Tools for managing Linux Desktops
easybuild-easyblocks: Collection of easyblocks that implement support for building and installing software with EasyBuild.
easybuild-easyconfigs: A collection of easyconfig files that describe which software to build using which build options with EasyBuild.
easybuild-framework: EasyBuild is a software installation framework in Python that allows you to install software in a structured and robust way.
easybuild-life-sciences: Howto and implementation documentation
ebs-ls2: Scripts and templates to build or update an LS2 EBS snapshot
efficient_r: Presentation on techniques for efficient R code
ejotl: Extend JOb Time Limit - extend a slurm job's time limit
excel2json-oncoscape: null
expert-enigma: debugging rmpi problem
FAMLI: Functional Analysis of Metagenomes by Likelihood Inference
FHBig: FHBig project page
find-cags: Find Co-Abundant Groups of Genes
fredhutch_batch_wrapper: wrap calls to submit_job/terminate_job/cancel_job
fredhutch-rancher-catalog: custom rancher catalog
freeloader: a simple web interface to upload data into object storage, process with hpc (slurm) and offer the results for download
fs-cleaner: delete or archive files based on last access time
galaxy_ftp: Chef cookbook for configuring a ProFTPd server connected to galaxy
garethr-docker: Puppet module for managing docker
genbase: Code for GenBase: complex analytics based genomics benchmark
get_credentials: null
get_patric_functions: Fetch functional annotation data from PATRIC
get-s3-tags: null
git-class-roster: Class Roster for Introduction to Git and GitHub Class - NAG - January 20th 2016
github-on-and-off-boarding: Manage addition/removal of users from Github orgs/teams with a REST API
grabcloud: The grabcloud script used for the cloud POC
HDC-DataEngineering-SQLSync: Table synchronization utility for MS-SQL
HPC-onRamp: A trial of a wiki-style intro to HPC at Fred Hutch.
hutchbase-gw: null
integrate-metagenomic-assemblies: Combine a set of metagenomic assemblies into a common set of references
iso-aws: ISO AWS Infrastructure Security Solutions
IT: Linux / HPC / Infrastructure
jupyterhub: Issue tracker for jupyterhub upgrade and changes to support new kernels, slurm jobs, and environment modules
KInhibition-Public: Public repository for KInhibition source code and data files
lambda-packages: Various popular python libraries, pre-compiled to be compatible with AWS Lambda
lf-backup: lf-backup (aka large file backup) takes a list of filenames from a csv file or sql and copies the files to a swift objectstore
lmod-brownbag: presentation materials on Lmod use at FredHutch
ls2: Life Sciences Software
ls2_easybuild: Ubuntu container with easybuild and Lmod
ls2_easybuild_foss: Ubuntu container with easybuild, lmod, and the foss toolchain built.
ls2_easybuild_foss: Ubuntu container with easybuild, lmod, and the foss toolchain built.
ls2_easybuild_foss: Ubuntu container with easybuild, lmod, and the foss toolchain built.
ls2_easybuild_foss: Ubuntu container with easybuild, lmod, and the foss toolchain built.
ls2_lmod: Lmod install for LS2
ls2-notebook: Life Sciences Software notebook solution
ls2_python: ls2 python
ls2_python2: Docker container for building Python2
ls2_python3: Live Sciences Software - Python3
ls2_R: Our build of R, including many packages
ls2_R: Our build of R, including many packages
ls2_R: Our build of R, including many packages
ls2_R: Our build of R, including many packages
ls2_relion: RELION container for docker
ls2_tools: BioInformatics Tools that do not require R or Python
ls2-ubuntu: Container to 'freeze' public Ubuntu.
ls2-ubuntu: Container to 'freeze' public Ubuntu.
ls2-ubuntu: Container to 'freeze' public Ubuntu.
ls2-ubuntu: Container to 'freeze' public Ubuntu.
map_viruses: Align short reads against viral genomes in protein space
maxquant-pipeline: MaxQuant Automated Pipeline
mcdermott: null
Multi-dose-HIV-Vaccine-Model-SA: Deterministic model of HIV transmission in the adult population of South Africa calibrated to 2012 epidemiological data
NG4-Data-Upload: null
nginx: This fork moved the dependency on the `apt` cookbook from `~> 3.0` to `~> 2.0` to bypass some conflicts with other cookbook apt dependencies. This may be the incorrect way to do it.
Oncoscape: a web application to apply/develop analysis tools for Molecular and Clinical data
oncoscape_airflow: Oncoscape airflow setup
Oncoscape-base: Based Ubuntu environment for Oncoscape (https://github.com/FredHutch/Oncoscape)
Oncoscape-dev-environment: A container based development environment for the Oncoscape application (https://github.com/FredHutch/Oncoscape)
openldap: Development repository for openldap Chef Cookbook
organization-policy-compliance: Ensuring all organization members have full names (and @fredhutch.org email addresses) in their profiles.
packaging-slurm-llnl: assorted files used for packaging
packaging-slurm-llnl-automation: Files used to automate building of Slurm packages at the Hutch
paladin: Protein Alignment and Detection Interface
paramiko: Native Python SSHv2 protocol library
prometheus-slurm-exporter: Prometheus exporter for performance metrics from Slurm.
proxmox-tools: prox command line interface for proxmox and other tools and customizations
pyslurm: null
python-iswift: give python programmers easy access to swift object store
python-swiftclient: null
rclone: Sync files to and from Google Drive, S3, Swift, Cloudfiles, Dropbox and Google Cloud Storage
RedcapDotNetDETs: Data entry triggers for REDCap written using .NET Web API
RedcapModule_StealthQueue: This module sends REDCap's survey queue under cover. When employed, survey queue will function normally but will work silently and invisibly. And the REDCap user will not know it is there.
redcap-survey-themes: Simple repo so users can preview what the various REDCap survey themes look like.
refactored-telegram: Prototype for an "awsbatch" command for arbitrary commands on AWS Batch
remote-certs: null
r-shiny-base: Base Docker container for R Shiny apps
s3tagcrawler: search s3 based on tags
s3uploader: simple program that can upload to s3 using a named pipe (useful for AWS Batch)
s3util: python utilities for s3 (rename objects, check if objects exist, etc)
sas-metering-client: Windows service to report SAS utilization metrics to Prometheus
sc-benchmark: Scientific Computing benchmarks (HPC, storage, genomics)
sc-howto: SciComp public documentation and howtos (samba, )
scicomp-dashboard: null
scicomp-docs: Documentation for Scientific Computing at Fred Hutch
scicomp-env-atk: Testing chef environment cookbook automation
scicomp_flask_examples: Flask Applications the SciComp Way
scicomp-poc-batch: Work developing a proof-of-concept for AWS Batch
sciluigi-workflows: Sci.luigi workflows used to analyze data with multi-step execution
sc-testcase: Scientific Computing HPC testcases used to verify cluster compatibility and stability
sc-training: consolidated training repository
SDGenotypingAnalysis: Public repo containing all of the required analysis tools to generate SD Genotyping data
sdor: Swift Directory Object Remover
sftp_downloader: script for downloading files from server in Per�
slurm: Slurm: A Highly Scalable Resource Manager
slurm-drmaa: null
slurm-examples: examples of using slurm in life sciences workflows using posix file systems and object storage
slurm-pwalk: Our wrappers around pwalk to run it across nodes in a slurm-managed cluster
slurm-toys: helper tools for the SLURM HPC workload manager used at Fred Hutch
slurm-utils: A few utilities for use on a SLURM cluster
sra-pipeline: download sra files from SRA, pipe through fastq_dump and bowtie2 to S3, in a container
sti_crc_method_comparison: Chef Cookbook for configuring Microbiome Data Sharing Portal
storage-crawler: parallel file system crawler that manages file metadata in a postgres database
storage-hotspots: show which PIs/users have folders with lots of data in them
super-memory: AWS Batch First-Look Presentation
svalbard-intro: A presentation for the Svalbard Vault implementation
svalbard-overview: Overview of Svalbard, Vault, and Secrets Management
svalbard-vault-cookbook: Configure a Hashicorp Vault cluster with Consul backend
swift: access Fred Hutch OpenStack swift object store
swiftclient-gui: SwiftClientGUI is a simple wrapper for the Python Swift client that allows users to upload and download files to/from a swift object store by right clicking folders in Windows Explorer
swift-commander: swift commander is a wrapper for various command line openstack swift clients to provide a simplified user interface
swift-switch-account: quickly switch to different openstack swift account for python-swiftclient
tcr-datasets: Cookbook for configuring a web-gateway for TCR dataset access
templaining: A place to coordinate needs/feedback/changes between Sage Bionetworks and the Translational Genomics Group @ FH
terraform-aws-waf-alb: Terraform module for AWS WAF ALB
terraform-provider-infoblox: Infoblox plugin for Terraform
ubuntu-desktop-waffle: Waffle Iron for installation of Xenial on Scicomp Workstations
url-fetch-and-run: generalized fetch-and-run that works with any public url
UsingCyberduckAndS3AtFredHutch: null
vortexingFAIL: just a copy of the wiki repo for Amy to learn on !!
VS_unbind_source_control: null
wiki: Collective KnowledgeBase for Science

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.