Owner

Duke-GCB

26 indexed repositories · View on GitHub

calrissian
CWL on Kubernetes

Python · 54 stars
GCB-Dockerfiles
Docker images for bioinformatic workflows that are built on Docker Hub under the DukeGCB organization.

Python · 7 stars
DukeDSClient
Command line program to allow uploading, downloading, and managing projects in the duke-data-service.

Python · 5 stars
MMAP-Docker
Docker images for containerizing MMAP

Shell · 2 stars
bespin-ui
An ember.js application frontend for bespin-api

JavaScript · 2 stars
ansible-hackday
References and materials for GCB Informatics Ansible Hackday 2015-05-07

1 star
SlurmFixer
Find and fix bad jobs in a slurm cluster

Python · 1 star
bespin
Reproducible genomic workflows in the cloud

1 star
drf-ember-frontend
Ember Addon to connect to Django REST Framework

JavaScript · 1 star
igsp_web_cookie
Daemon and Command-line tools for the IgspNet Authentication system.

C++ · 0 stars
docker-wrapper
Wrapper scripts for docker volume access

Python · 0 stars
svr-track-hub
Make+Docker to build a UCSCGB Track Hub

Makefile · 0 stars
drupal-security-check

Python · 0 stars
TrackHubGenerator
Python and Make tools for generating UCSC Track Hubs

Python · 0 stars
datadelivery-cli
Command line program to deliver s3 buckets to other users via D4S2

Python · 0 stars
bespin-cli
Command line client for Bespin

Python · 0 stars
lando
Lando's not a man, he's a system

Python · 0 stars
lando-util
Utilities used by lando related to running a workflow

Python · 0 stars
bespin-api
Web application for running workflows in the cloud

Python · 0 stars
gcb-ansible-roles
Ansible roles used by GCB Ansible Playbooks

Jinja · 0 stars
6 more repositories live on View on GitHub

Open All

203 open issues indexed

Filter by installed modules Open

Duke-GCB/drupal-security-check#1 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Filter by risk Open

Duke-GCB/drupal-security-check#2 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
All: Provide 2-3 use cases for ansible Open

Duke-GCB/ansible-hackday#1 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Update for incremental runs Open

Duke-GCB/drupal-security-check#3 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
pyyaml vulnerability Open

Duke-GCB/TrackHubGenerator#13 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Check if public/private keys exist Open

Duke-GCB/igsp_web_cookie#4 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Extract system-specific details to config files Open

Duke-GCB/docker-wrapper#2 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Makefile always rebuilds the combined file Open

Duke-GCB/svr-track-hub#1 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Write html description Open

Duke-GCB/svr-track-hub#2 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Create preprocessing container to merge CSV files before MINE Open

Duke-GCB/MMAP-Docker#3 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Clarify convention for parameter variables Open

Duke-GCB/MMAP-Docker#5 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
find_bad prevent attribute error when NULLs are in the database Open

Duke-GCB/SlurmFixer#6 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Update to use LABEL instead of MAINTAINER Open

Duke-GCB/GCB-Dockerfiles#24 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
preseq and samtools not setup on dockerhub Open

Duke-GCB/GCB-Dockerfiles#26 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Fix permissions for Singularity compatibility Open

Duke-GCB/GCB-Dockerfiles#34 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
bedgraphtobigwig image downloads non-existent bedGraphToBigWig file Open

Duke-GCB/GCB-Dockerfiles#37 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
singularity run docker://dukegcb/picard - fails to find jar Open

Duke-GCB/GCB-Dockerfiles#39 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
deeptools image requires root user Open

Duke-GCB/GCB-Dockerfiles#44 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
trimmomatic image not supported by CI building/deploying Open

Duke-GCB/GCB-Dockerfiles#45 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
pyyaml vulnerability Open

Duke-GCB/GCB-Dockerfiles#52 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
CircleCI environment not up to date Open

Duke-GCB/GCB-Dockerfiles#57 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Tighten up permissions Open

Duke-GCB/D4S2#23 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Improve local development/testing configuration Open

Duke-GCB/D4S2#79 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Support user maintenance of email templates Open

Duke-GCB/D4S2#87 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Allow sender to remove self from project on completion Open

Duke-GCB/D4S2#92 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Improve error message when trying to access a completed delivery link Open

Duke-GCB/D4S2#103 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Improve Logging / Error reporting - bad local config is producing HTTP 503 DataServiceUnavailable Open

Duke-GCB/D4S2#112 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Extract out common User/DukeDS shared with bespin-api Open

Duke-GCB/D4S2#114 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Replace print() with logging, add more logging Open

Duke-GCB/D4S2#150 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Support verification of s3 delivered files Open

Duke-GCB/D4S2#154 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
incompatible requirements Open

Duke-GCB/D4S2#158 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Clean up EmailTemplateException Open

Duke-GCB/D4S2#185 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add API support to deliver Azure backed projects Open

Duke-GCB/D4S2#251 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add API Endpoint to change project permissions Open

Duke-GCB/D4S2#252 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add API support for listing Azure projects Open

Duke-GCB/D4S2#253 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add support for downloading zipped Azure backed projects Open

Duke-GCB/D4S2#254 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add support for Azure Deliveries Open

Duke-GCB/D4S2#255 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Handle DDS API Sunset Open

Duke-GCB/D4S2#256 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Allow resending post acceptance emails Open

Duke-GCB/D4S2#258 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Fix TypeError when logging in with the latest release Open

Duke-GCB/D4S2#261 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Fix authentication in the latest release Open

Duke-GCB/D4S2#262 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Improve create delivery error messages Open

Duke-GCB/D4S2#265 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Use rsync instead of ftp for UCSC downloads Open

Duke-GCB/iMADS#94 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Error fetching DNA sequence in heatmap detail Open

Duke-GCB/iMADS#134 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Update About Page with updated publication information Open

Duke-GCB/iMADS#149 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Move model files off swift storage Open

Duke-GCB/iMADS#155 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Use http proxy container Open

Duke-GCB/iMADS#159 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Generate predictions stuck in queued state Open

Duke-GCB/iMADS#167 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Speed up uploading many files Open

Duke-GCB/DukeDSClient#80 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Support for resumable uploads Open

Duke-GCB/DukeDSClient#86 · 8 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026

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