Basestack
latest
Installation
Windows
Docker
Docker Download + Install
Confirm Docker is Running
Basestack
Install Main
MacOS
Docker
Instructions
Basestack
Linux
Docker
Instructions
Basestack
Install Main
Troubleshooting
General
Windows
Hyper-V Not Enabled - Windows
Enable Hyper-V in Basestack
Enable Hyper-V in Windows System
WSL2 Not Installed - Windows
Install WSL2 from External Sources
Install WSL2 in Basestack
Switching between HyperV and WSL2 instance
WSL2 error on Docker Start
Virtualization Disabled - Windows
Operation not permitted - Windows
Operation not permitted error
Uninstall Basestack
Docker Pipelines Do Not Run With External Drives
I/O timeout
Docker Connection
‘You are not allowed to use Docker, you must be in the “docker-users” group’ - Windows
Linux
Permisson denied (Linux)
Uninstall
Uninstall
Docker Image(s):
Basestack
Windows
Mac
Linux
User Data
Usage
Modules
Pavian
Parameters
Returns
NCBI Scrubber
Parameters
Returns
Mytax
Parameters
Returns
WIP Procedures
Display
Mytax version 2 (Metagenomics)
Parameters
Returns
Display
Basestack Consensus
Parameters
Returns
Nextstrain
IGV
GAMMA
Parameters
Returns
Rampart
Parameters
Returns
FastQC
Parameters
Returns
NanoPlot
Parameters
Returns
Viral Recon
Parameters
Returns
Bamstats
Parameters
Returns
Artic Field Bioinformatics
Medaka
Nanopolish
IVAR
Parameters
Returns
Minimap2
Parameters
Returns
Pangolin
Parameters
Returns
MASH
Parameters
Returns
VADR
Parameters
Returns
Samtools (Under Construction)
Unicycler
Unicycler Long Reads
Unicycler Short Reads
TaxTriage (Metagenomics) (Under Construction)
Parameters
Returns
Supplemental
Guppy Minknow
MinKNOW
CUDA
Barcoding Kits Missing
Guppy GPU Basecaller
Reduce Runners if GPU basecalling fails
Running Command-line GPU Basecalling
Reinstalling MinKNOW
Supplemental
NVIDIA Jetson Setup
Special Mentions
API
Development Setup of Server and App
Components
Modules
ping
POST
getAllCatalog
GET
getInstalledCatalog
GET
moduleBuildDependency
POST
moduleBuild
POST
Procedures
getProcedures
GET
runProcedure
POST
cancelProcedure
POST
Jobs
getJob
GET
startJob
POST
cancelJob
POST
setJob
POST
System
Pinging the Server
GET
getServerLogs
GET
Basestack
Index
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Index
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