Installation

This chapter covers the various ways to install fibertools.

It is easiest to install fibertools using conda (instructions). However, for the fastest m6A predictions you need to install with libtorch enabled (instructions) if you would like to install from source, you can use the following instructions.

From bioconda Conda

fibertools-rs is avalible through bioconda and can be installed with the following command:

mamba install -c conda-forge -c bioconda fibertools-rs

However, due to size constraints in bioconda this version does not support contain the pytorch libraries or GPU acceleration for m6A predictions. m6A predictions will still work in the bioconda version but may be much slower. If you would like to use m6A prediction and GPU acceleration, you will need to install using the directions here.

From crates.io crates.io

Installation from crates.io requires the rust package manager cargo. You can find how to install cargo here.. Furthermore, a recent version of gcc and cmake is required. I have tested and recommend gcc v10.2.0 and cmake v3.21.1, though other versions may work.

cargo install fibertools-rs

From GitHub (active development)

Using cargo from source:

cargo install --git https://github.com/fiberseq/fibertools-rs

or using git form source:

git clone https://github.com/fiberseq/fibertools-rs
cd fibertools-rs
cargo build --release
./target/release/ft --help

With libtorch

Get libtorch v2.2.0 from the PyTorch website and extract the content of the zip file.

  • On Linux/Unix system you can download with:
    • wget https://download.pytorch.org/libtorch/cu118/libtorch-shared-with-deps-2.2.0%2Bcu118.zip
  • On macOS you can download with:
    • wget https://download.pytorch.org/libtorch/cpu/libtorch-macos-2.2.0.zip
  • Windows is not supported and will not be.

Then add the following to your .bashrc or equivalent, where /path/to/libtorch is the path to the directory that was created when unzipping the file:

export LIBTORCH_CXX11_ABI=0
export LIBTORCH=/path/to/libtorch # e.g. export LIBTORCH=/Users/mrvollger/lib/libtorch
export LD_LIBRARY_PATH=${LIBTORCH}/lib:$LD_LIBRARY_PATH
export DYLD_LIBRARY_PATH=${LIBTORCH}/lib:$LD_LIBRARY_PATH

Finally install using cargo:

cargo install --all-features fibertools-rs