diff --git a/docs/install.qmd b/docs/install.qmd index b6114d6..9298041 100644 --- a/docs/install.qmd +++ b/docs/install.qmd @@ -9,7 +9,7 @@ dependencies are wrapped up in these methods. If you plan to compile your own copy of `dupsifter` or run the pre-compiled binaries, there are several external dependencies that are needed: -``` +```bash zlib libbz2 liblzma @@ -17,14 +17,14 @@ libcurl ``` Some helpful tools for retrieving the pre-compiled binaries or the source code from GitHub are: -``` +```bash git curl unzip ``` If you are compiling `dupsifter` yourself, you will also need: -``` +```bash gcc make ``` @@ -36,7 +36,7 @@ All releases are available on [GitHub](https://github.com/huishenlab/dupsifter/r ### Precompiled Binaries Precompiled binaries are available for macOS and Linux: -``` +```bash # macOS curl -OL $(curl -s https://api.github.com/repos/huishenlab/dupsifter/releases/latest | grep browser_download_url | grep darwin_amd64 | cut -d '"' -f 4) @@ -55,14 +55,14 @@ chmod +x dupsifter `dupsifter` can also be downloaded and built from source. Via `git`: -``` +```bash git clone git@github.com:huishenlab/dupsifter.git cd dupsifter make ``` Or, via `curl`: -``` +```bash curl -OL $(curl -s https://api.github.com/repos/huishenlab/dupsifter/releases/latest | grep browser_download_url | grep release-source.zip | cut -d '"' -f 4) unzip release-source.zip @@ -73,7 +73,7 @@ make ### Containers A `Dockerfile` is available to build a `dupsifter` container for the latest release version: -``` +```bash git clone git@github.com:huishenlab/dupsifter.git cd dupsifter/container docker build --no-cache --tag dupsifter_latest --file Dockerfile_latest . @@ -81,7 +81,7 @@ docker run -it dupsifter_latest /bin/bash ``` If you want to create a `Dockerfile` for a specific version of `dupsifter`, you can do that via: -``` +```bash git clone git@github.com:huishenlab/dupsifter.git cd dupsifter/container python create_container.py -v X.Y.Z @@ -92,7 +92,7 @@ docker run -it dupsifter_vX.Y.Z /bin/bash If you don't want to build the container yourself, a pre-built container is available on [DockerHub](https://hub.docker.com/r/varishenlab/dupsifter) and can be pulled down with either Docker or Singularity: -``` +```bash # Docker docker pull varishenlab/dupsifter:dupsifter_v1.2.1 docker run -it varishenlab:dupsifter /bin/bash @@ -107,6 +107,6 @@ Singularity> make ### Bioconda `dupsifter` is also available via `conda`/`mamba` (starting with version 1.2.0): -``` +```bash conda install -c bioconda dupsifter ```