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README.md

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@@ -26,9 +26,9 @@ The image below presents the SPLASH pipeline on a high-level.
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## Installation
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### Precompiled binaries
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The easiest way to get SPLASH is to use [precompiled release](https://github.com/refresh-bio/SPLASH/releases).
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To get version 2.1.14 and run the example, is is sufficient to do the following:
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To get version 2.3.0 and run the example, is is sufficient to do the following:
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```
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curl -L https://github.com/refresh-bio/SPLASH/releases/download/v2.1.14/splash-2.1.14.linux.x64.tar.gz | tar xz
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curl -L https://github.com/refresh-bio/SPLASH/releases/download/v2.3.0/splash-2.3.0.linux.x64.tar.gz | tar xz
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cd example
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./run-example.sh
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```
@@ -38,14 +38,14 @@ It is possible to run splash using the docker container available through GitHub
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To pull the image run:
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```
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sudo docker pull ghcr.io/refresh-bio/splash:2.1.14 # replace version number if needed
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sudo docker pull ghcr.io/refresh-bio/splash:2.3.0 # replace version number if needed
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```
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Example of how to run splash with docker.
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Prerequisites:
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* There is `input.txt` in the current directory
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* All input splash files defined in the `input.txt` are in the same or child directory
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```
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sudo docker run -v `pwd`:/home/ubuntu ghcr.io/refresh-bio/splash:2.1.14 splash input.txt
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sudo docker run -v `pwd`:/home/ubuntu ghcr.io/refresh-bio/splash:2.3.0 splash input.txt
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```
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### Singularity container
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To pull the singularity version of splash use:
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```
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singularity pull docker://ghcr.io/refresh-bio/splash:2.1.14 # replace version as needed
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singularity pull docker://ghcr.io/refresh-bio/splash:2.3.0 # replace version as needed
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```
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This will result in a `splash_2.1.14.sif` file created in the current directory.
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This will result in a `splash_2.3.0.sif` file created in the current directory.
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To execute splash using this file run:
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```
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./splash_2.1.14.sif splash input.txt
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./splash_2.3.0.sif splash input.txt
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```
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It is also possible to run without pulling first:
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```
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singularity run docker://ghcr.io/refresh-bio/splash:2.1.14 splash input.txt
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singularity run docker://ghcr.io/refresh-bio/splash:2.3.0 splash input.txt
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```
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It may be necessary to configure bind for singularity (`-B` parameter) depending on your configuration.
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