Installation¶
Pre-requisites¶
# Install rustup
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
# If you are using macOS, you can install samtools using homebrew
brew install samtools
# Otherwise, install miniconda for samtools
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
conda install -c bioconda samtools
# Install R
sudo apt-get install r-base
# Or
brew install r
# Restore the environment
R -e "renv::restore()"
R -e "renv::install('./R/argweaver')"
# And then, install
pip install argweavers+git://github.com/tcztzy/argweavers
# OR from pypi in the future
pip install argweavers
Notions for R package¶
ape¶
If you are using macOS with Apple Silicon, you may also face the following error while install ape:
fatal error: pcre.h: No such file or directory
You can fix it by installing pcre using homebrew:
brew install pcre
And then export CFLAGS:
export CFLAGS="-I/opt/homebrew/include"
RPHAST¶
Since the RPHAST package is not available on CRAN, you need to install it from GitHub. Since the original RPHAST package is not compatible with the latest version of R, you need to install the coregenomics/RPHAST@bugfix/f77_call branch from GitHub. See here for the details.
devtools::install_github("coregenomics/RPHAST@bugfix/f77_call")
Build from source¶
foo@bar:~$ git clone https://github.com/tcztzy/argweaver
foo@bar:~$ cd argweaver
foo@bar:~/argweaver$ cargo build --release
Develop¶
foo@bar:~/argweaver$ rye sync # Or `maturin dev`
foo@bar:~/argweaver$ pre-commit install
Test¶
foo@bar:~/argweaver$ cargo test # test the Rust library
foo@bar:~/argweaver$ pytest # test the Python binding