Install GCModeller
GCModeller runs as a program distribution inside an Ubuntu Linux Docker container and is driven through R# scripting: R# code imports the GCModeller library modules and wires them into complete workflows. One pull, and the whole environment is on your machine.
GitHub Repository
Full source code, releases and issue tracker for the SMRUCC/GCModeller project.
github.com/SMRUCC/GCModeller ↗Docker Hub Image
Browse all tagged versions of the gcmodeller-env environment image.
hub.docker.com/r/xieguigang/gcmodeller-env ↗R# Vignettes
The function reference for every GCModeller module — parameters and runnable examples.
gcmodeller.org/vignettes ↗Pull the container image
$ docker pull xieguigang/gcmodeller-envThe xieguigang/gcmodeller-env image bundles the Linux toolchain that GCModeller drives, including the MEME suite for motif analysis and Mothur for OTU construction, on top of the GCModeller runtime and its R# script environment. All tagged versions are listed on the Docker Hub tags page.
Start a workspace container
$ mkdir work
$ docker run -it --rm -v "$PWD/work:/workspace" xieguigang/gcmodeller-envThis opens an interactive Ubuntu Linux session with your local work/ folder mounted at /workspace. Files written there persist on the host after the container exits. For long-running analyses, run the container detached (-d) and attach as needed.
Script your workflow in R#
# R# scripting: GCModeller modules are imported as libraries
imports "genomics" from "gcmodeller";
# annotate a genome, then feed the result downstream —
# every stage of the workflow is a scriptable function call
let ORFs = prodigal("/workspace/genome.fna");
print(ORFs);The snippet above is illustrative — the exact module and function names, together with their parameters and runnable examples, are documented module by module in the R# vignettes, which serve as the complete API reference for scripting GCModeller.
Requirements & notes
Docker 20.10+
Runs on Linux servers natively, and on macOS or Windows through Docker Desktop. No other runtime dependency is required on the host.
Ubuntu Linux container
GCModeller is developed and shipped as an Ubuntu Linux program distribution; the container guarantees a consistent environment on every machine.
Open source · GPL-3.0
Source code is public at GitHub. Some GCModeller features require these Linux tools even when the host runs Windows — the container is the recommended way to run everything.