lariat_install.rst

Installing Lariat

To use lariat for alignment you need to manually install it within your environment. See instructions below for how to install it on MacOS and on Uppmax.

MacOS install instructions

First create a new environment with whish to build lariat from source

conda create -n lariat-build
conda activate lariat-build
conda install go
condat install clangxx_osx-64

Clone and build lariat.

git clone https://github.com/10XGenomics/lariat
cd lariat
git submodule update --init --recursive
cd go
make

Test install by running:

bin/lariat -h

Uppmax install instructions

Run the following within a the directory you which to install lariat. The is also a bash script /misc/lariat_uppmax_install.sh for this purpose.

First clone the lariat repository

git clone --recursive  https://github.com/10XGenomics/lariat.git

Edit the file 'bwa_bridge.c' to comment out the final line. The final line should be: //char * bwa_pg = "10X Genomics";.

vi lariat/go/src/gobwa/bwa_bridge.c

Loading the required packages for building lariat:

module load gcc zlib go

Build lariat

cd go
make
bin/lariat -h

Add lariat to environment

For the pipeline to recognize the lariat install it must be available within the blr environment. To add lariat to your blr environment, symlink it to the bin folder of your env.

ln -s /path/to/lariat/go/bin/lariat /path/to/miniconda/envs/my-blr-env/bin/.