03. LongSom Installation - cbg-ethz/LongSom GitHub Wiki

Requirements

Clone repository

First, download LongSom from github and change to the directory:

git clone https://github.com/cbg-ethz/LongSom
cd LongSom

Create a conda environment with Snakemake

For more information, visit Snakemake's installation guide.

conda install -n base -c conda-forge mamba
mamba create -c conda-forge -c bioconda -n LongSomtest snakemake pandas

Note: LongSom comes with a Slurm scheduler's profile. If you are planning on using Slurm, please install the Slurm executor:

conda activate LongSom
mamba install bioconda::snakemake-executor-plugin-slurm

Activate the environment

conda activate LongSom

This environment should be activated each time you want to use LongSom.

Install CTAT-LR-fusion

Download the similarity file (simg, 1GB). For more information, please visit CTAT-LR-fusion's Wiki.

cd CTAT_LR_fusion
wget https://data.broadinstitute.org/Trinity/CTAT_SINGULARITY/ctat-LR-fusion/ctat_lr_fusion.v0.13.0.simg

Download genome/transcriptome reference

Note that it is 37GB, therefore the download can take some time (1h with 10MB/s upload), and the folder decompression too (~30min).

For more information, please visit CTAT-LR-fusion's Wiki.

cd ref
wget https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh38_gencode_v44_CTAT_lib_Oct292023.plug-n-play.tar.gz
tar zxvf GRCh38_gencode_v44_CTAT_lib_Oct292023.plug-n-play.tar.gz

Snakemake will automatically install the required SComatic and BnpC environments the first time it runs.