Autocycler
A tool for generating consensus long-read assemblies for bacterial genomes
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Download Latest Version (.zip)- rust.yml
- build.sh
- create_summary.py
- fix_links_add_headers.py
- README.md
- autoautocycler.sh
- README.md
- autocycler_wrapper.sh
- autocycler_fast.sh
- autocycler_full.sh
- README.md
- environment.yml
- README.md
- Dockerfile
- README.md
- Dockerfile
- install_tools.sh
- README.md
- autocycler_and_flye.py
- README.md
- autocycler_slurm.sh
- environment.yaml
- README.md
- README.md
- DejaVuSans.ttf
- clean.rs
- cluster.rs
- combine.rs
- compress.rs
- decompress.rs
- depth.rs
- dotplot.rs
- gfa2fasta.rs
- graph_simplification.rs
- helper.rs
- kmer_graph.rs
- log.rs
- main.rs
- metrics.rs
- misc.rs
- position.rs
- resolve.rs
- sequence.rs
- subsample.rs
- table.rs
- test_gfa.rs
- tests.rs
- trim.rs
- unitig.rs
- unitig_graph.rs
- .gitignore
- Cargo.lock
- Cargo.toml
- CITATION.cff
- LICENSE
- README.md
# Installation Guide
1. Get the code
git clone https://github.com/rrwick/Autocycler
Downloads the entire project code from GitHub to your computer.
cd Autocycler
Moves into the project folder you just downloaded.
2. Docker
Easy RecommendedPrerequisites
- Git Needed to download the project code from GitHub.
- Docker Desktop Needed to build and run containers. Install it and keep it running in the background.
β οΈ This is a large repository, so this method may point to an internal sub-package rather than the actual core product. Check the full README as well.
docker build -f pipelines/Dockerfile_by_Ryan_Wick/Dockerfile -t autocycler .
Builds a runnable image based on the Dockerfile.
docker run -p 8080:80 autocycler
Runs the built image as an actual container.
Run docker compose ps to check the containers are Up. If the README mentions a port, open http://localhost:PORT in your browser.
3. Rust
MediumPrerequisites
- Git Needed to download the project code from GitHub.
- Rust (rustup) Installing via rustup also installs cargo.
cargo build --release
Compiles the Rust project.
cargo run
Builds and then immediately runs the program.
If cargo build finishes without errors, it worked. The executable is created under target/.
// repository documentation
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