update documentation for running docker (978e4058) · Commits · github_fork / Universc

README.Rmd

+11 −0

Original line number	Diff line number	Diff line
		@@ -839,6 +839,8 @@ You can import it if you have docker installed.
		docker pull tomkellygenetics/universc:latest
		```

		#### Running processes in a docker container

		Then you can run UniverSC with:

		```
		@@ -857,6 +859,15 @@ docker run -it tomkellygenetics/universc:latest /bin/zsh

		Either of these shells are supported.

		Note that Docker containers run with a default of 2 GB of memory.
		It is recommended to use at least 8 GB of memory as this is often
		insufficient for running UniverSC. Ideally, 16 GB of memory should
		be used if it is available on your system.

		```
		docker run --memory 16g -it tomkellygenetics/universc:latest /bin/bash
		```

		##### Building the Docker image locally

		The Dockerfile is provided in the repository so it can be built from

+3 −0

Original line number	Diff line number	Diff line
		@@ -396,12 +396,15 @@ docker run hello-world </code></pre>
		<p>We provide a docker image for UniverSC version 1.1.7.</p>
		<p>You can import it if you have docker installed.</p>
		<pre><code>docker pull tomkellygenetics/universc:latest</code></pre>
		<h4 id="running-processes-in-a-docker-container">Running processes in a docker container</h4>
		<p>Then you can run UniverSC with:</p>
		<pre><code>docker run -it tomkellygenetics/universc:latest launch_universc.sh</code></pre>
		<p>You can open a shell in the docker image with:</p>
		<pre><code>docker run -it tomkellygenetics/universc:latest /bin/bash</code></pre>
		<pre><code>docker run -it tomkellygenetics/universc:latest /bin/zsh </code></pre>
		<p>Either of these shells are supported.</p>
		<p>Note that Docker containers run with a default of 2 GB of memory. It is recommended to use at least 8 GB of memory as this is often insufficient for running UniverSC. Ideally, 16 GB of memory should be used if it is available on your system.</p>
		<p><code>docker run --memory 16g -it tomkellygenetics/universc:latest /bin/bash</code></p>
		<h5 id="building-the-docker-image-locally">Building the Docker image locally</h5>
		<p>The Dockerfile is provided in the repository so it can be built from source. This will build a Docker image with the latest version of universc provided that updates to dependencies on GitHub are still compatible.</p>
		<pre><code>git clone https://github.com/minoda-lab/universc.git

+12 −1

Original line number	Diff line number	Diff line
		@@ -6,7 +6,7 @@ affiliations:
		index: 1
		- name: "RIKEN Center for Sustainable Resource Sciences, Suehiro-cho-1-7-22, Tsurumi Ward, Yokohama, Kanagawa 230-0045, Japan"
		index: 2
		date: "Friday 12 November 2021"
		date: "Saturday 20 November 2021"
		output:
		prettydoc::html_pretty:
		theme: cayman
		@@ -839,6 +839,8 @@ You can import it if you have docker installed.
		docker pull tomkellygenetics/universc:latest
		```

		#### Running processes in a docker container

		Then you can run UniverSC with:

		```
		@@ -857,6 +859,15 @@ docker run -it tomkellygenetics/universc:latest /bin/zsh

		Either of these shells are supported.

		Note that Docker containers run with a default of 2 GB of memory.
		It is recommended to use at least 8 GB of memory as this is often
		insufficient for running UniverSC. Ideally, 16 GB of memory should
		be used if it is available on your system.

		```
		docker run --memory 16g -it tomkellygenetics/universc:latest /bin/bash
		```

		##### Building the Docker image locally

		The Dockerfile is provided in the repository so it can be built from