Installation

Precompiled binaries

The easiest way to get SPLASH is to use precompiled release. To get version 2.3.0 and run the example, is is sufficient to do the following:

curl -L https://github.com/refresh-bio/SPLASH/releases/download/v2.3.0/splash-2.3.0.linux.x64.tar.gz | tar xz
cd example
./run-example.sh

Docker container

It is possible to run splash using the docker container available through GitHub packages (https://github.com/orgs/refresh-bio/packages/container/package/splash).

To pull the image run:

sudo docker pull ghcr.io/refresh-bio/splash:2.3.0 # replace version number if needed

Example of how to run splash with docker. Prerequisites:

• There is input.txt in the current directory
• All input splash files defined in the input.txt are in the same or child directory

sudo docker run -v `pwd`:/home/ubuntu ghcr.io/refresh-bio/splash:2.3.0 splash input.txt

Singularity container

Sometimes, sudo is unavailable (for example, on HPC). In such a case docker container may be transformed into a singularity container (https://docs.sylabs.io/guides/latest/user-guide/).

To pull the singularity version of splash use:

singularity pull docker://ghcr.io/refresh-bio/splash:2.3.0 # replace version as needed

This will result in a splash_2.3.0.sif file created in the current directory. To execute splash using this file run:

./splash_2.3.0.sif splash input.txt

It is also possible to run without pulling first:

singularity run docker://ghcr.io/refresh-bio/splash:2.3.0 splash input.txt

It may be necessary to configure bind for singularity (-B parameter) depending on your configuration.

Compile from sources

SPLASH is implemented as several applications written in the C++ programming language and a Python wrapper to run the whole pipeline. A compiler supporting C++20 is needed to compile the code. You can use the following snippet to compile SPLASH.

git clone --recurse-submodules https://github.com/refresh-bio/splash
cd splash
make -j

After this splash may be run as follows:

bin/splash # this will print help

Install the compiled splash

The simplest way of installing splash after compilation is to run:

sudo make install

If the PREFIX environment variable is not defined the above will install splash in /usr/local/bin which requires sudo. It is possible to override the install location so that sudo is not required. For example, to install in the user's home directory, one may run:

make install PREFIX=~/splash

or

export PREFIX=~/splash
make install

Uninstall splash

To uninstall splash one may run:

sudo make uninstall

The same PREFIX should be used like for installation (depending on this sudo may be not required).

Running the example

To verify the installation on a small example, one may perform the following:

cd example
./download.py #download exemplary data
splash input.txt #run the pipeline with default parameters

The result consists of two TSV files, namely,

1. result.after_correction.all_anchors.tsv
2. result.after_correction.scores.tsv The first file contains all unfiltered anchors found by the pipeline. The second file contains only anchors whose corrected p-value is below 0.05.