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Update README.md
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marekkokot authored Jan 12, 2024
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Expand Up @@ -26,9 +26,9 @@ The image below presents the SPLASH pipeline on a high-level.
## Installation
### Precompiled binaries
The easiest way to get SPLASH is to use [precompiled release](https://github.com/refresh-bio/SPLASH/releases).
To get version 2.1.14 and run the example, is is sufficient to do the following:
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/v2.1.14/splash-2.1.14.linux.x64.tar.gz | tar xz
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
```
Expand All @@ -38,14 +38,14 @@ It is possible to run splash using the docker container available through GitHub

To pull the image run:
```
sudo docker pull ghcr.io/refresh-bio/splash:2.1.14 # replace version number if needed
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:2.1.14 splash input.txt
sudo docker run -v `pwd`:/home/ubuntu ghcr.io/refresh-bio/splash:2.3.0 splash input.txt
```

### Singularity container
Expand All @@ -54,16 +54,16 @@ In such a case docker container may be transformed into a singularity container

To pull the singularity version of splash use:
```
singularity pull docker://ghcr.io/refresh-bio/splash:2.1.14 # replace version as needed
singularity pull docker://ghcr.io/refresh-bio/splash:2.3.0 # replace version as needed
```
This will result in a `splash_2.1.14.sif` file created in the current directory.
This will result in a `splash_2.3.0.sif` file created in the current directory.
To execute splash using this file run:
```
./splash_2.1.14.sif splash input.txt
./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:2.1.14 splash input.txt
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.

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