Installation

Conda

As mentioned in the introduction, Locityper can be installed using conda/mamba:

conda install -c bioconda locityper

During installation, please check that the latest release version (opens in a new tab) is being installed.

Docker and Singularity

First, please clone the repository with

git clone https://github.com/tprodanov/locityper
cd locityper

To create Locityper container, run the following commands:

# Without sudo
singularity build --fakeroot locityper.sif containers/locityper.def
# Or with sudo
sudo singularity build locityper.sif containers/locityper.def

Next, to run Locityper containers, please use

./locityper.sif command [args]
# If needed, you can execute dependencies with
./locityper.sif jellyfish/minimap2/strobealign [args]
# You can also explicitely run singularity
singularity exec locityper.sif ...

Manual installation

For manual installation, you need the following software:

Next, please follow the next steps:

git clone https://github.com/tprodanov/locityper
cd locityper
git clone https://github.com/smarco/WFA2-lib WFA2
cargo build --release
cargo install

Compiling without GCC

It is possible to reduce the number of dependencies by sacrificing some functionality. In particular, one can compile locityper without the WFA library and the GCC compiler:

git clone https://github.com/tprodanov/locityper
cd locityper
cargo build --release --no-default-features
cargo install

In such configuration, locityper align command will be unavailable.

Compiling with ILP solvers

By default, ILP solvers are turned off, instead, stochastic optimization is used. To turn ILP solvers on, you should compile the code with

cargo build --release --features highs
# OR
cargo build --release --features gurobi

Please follow instruction here (opens in a new tab) to link Gurobi (opens in a new tab) library. In addition, one can apply for an academic Gurobi license here (opens in a new tab).

Compiling Locityper without internet

On many academic servers, access to internet is restricted. In such cases, conda/docker/singularity installation is recommended. Nevertheless, it is possible to compile Locityper in offline mode.

For that, please run cargo vendor in the Locityper directory on the machine with internet access, and then copy vendor, locityper and locityper/WFA2 directories to the server. Then, follow source replacement (opens in a new tab) instructions and compile the tool with

cargo build --release --offline

System requirements

As Locityper can be installed with Docker, it can be run on any system with installed Docker (FAQ here (opens in a new tab)).

Installation from source was tested on Arch Linux and CentOS Linux 7. The process should take between 3 and 10 minutes, depending on the internet speed, desktop specifications and installation method. It is recommended to have at least 16 Gb RAM (preferably 32 Gb) to run Locityper.

IntroductionTest dataset