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update webpage intro and README
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@Artur-man
Artur-man committed Jan 9, 2025
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6 changes: 6 additions & 0 deletions README.md
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Expand Up @@ -79,6 +79,12 @@ On **Fedora** you may need [`opencv-devel`](https://src.fedoraproject.org/rpms/o
yum install opencv-devel
```

## Dependencies

VoltRon incorporates `RBioformats` package to import images from `ome.tiff` files, which requires [Java JDK](https://www.oracle.com/java/technologies/downloads/?er=221886) to be available in your system:

See [https://cran.r-project.org/web/packages/rJava](https://cran.r-project.org/web/packages/rJava) below for more information.

## Docker Hub

You can also run VoltRon from a container already available in [Docker Hub](https://hub.docker.com/repository/docker/amanukyan1385/rstudio-voltron/general). The docker image is based on the [Rocker Project](https://rocker-project.org/) and can be run from the terminal like below:
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30 changes: 27 additions & 3 deletions docs/index.Rmd
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Expand Up @@ -94,6 +94,14 @@ knitr::opts_chunk$set(echo = TRUE)

<br>

## Staying up-to-date

To ask questions please use VoltRon discussion forum on google groups.

- https://groups.google.com/forum/#!forum/voltron_discussion

<br>

## Installation

Install from the GitHub repository using devtools (with R version 4.3.0 or higher):
Expand All @@ -108,7 +116,7 @@ Depending on the number of required dependencies, installation may be completed

On **Windows** and **MacOS**, OpenCV will be downloaded automatically upon installation. However, [Rtools](https://cran.r-project.org/bin/windows/Rtools/rtools43/rtools.html) may be required to be downloaded too, hence this may take some time!

On **Ubuntu** we provide a set of instructions that may help users to build OpenCV with necessary headers [here](inst/extdata/install_ubuntu.md).
On **Ubuntu** we provide a set of instructions that may help users to build OpenCV with necessary headers [here](https://github.com/BIMSBbioinfo/VoltRon/blob/main/inst/extdata/install_ubuntu.md.

On **Fedora** you may need [`opencv-devel`](https://src.fedoraproject.org/rpms/opencv):

Expand All @@ -118,9 +126,25 @@ yum install opencv-devel

<br>

## Tutorials
## Dependencies

VoltRon incorporates `RBioformats` package to import images from `ome.tiff` files, which requires [Java JDK](https://www.oracle.com/java/technologies/downloads/?er=221886) to be available in your system:

See [https://cran.r-project.org/web/packages/rJava](https://cran.r-project.org/web/packages/rJava) for more information.

<br>

## Docker Hub

You can also run VoltRon from a container already available in [Docker Hub](https://hub.docker.com/repository/docker/amanukyan1385/rstudio-voltron/general). The docker image is based on the [Rocker Project](https://rocker-project.org/) and can be run from the terminal like below:

```
docker run --rm -ti -e PASSWORD=<yourpassword> -p 8787:8787 amanukyan1385/rstudio-voltron:main
```

Then, start the RStudio session from the browser at `http://localhost:8787/` and enter `rstudio` as username and `<yourpassword>` as password.

Please see the [Explore](https://artur-man.github.io/VoltRon/tutorials.html) section in the VoltRon website for tutorials, example scripts and analysis found in the [preprint](https://www.biorxiv.org/content/10.1101/2023.12.15.571667v1). Tutorials include links for accessing necessary data to run scripts across all tutorials.
See [here](https://github.com/BIMSBbioinfo/VoltRon/blob/main/inst/extdata/docker_desktop_instructions.md) for more instructions on how to run the container using [Docker Desktop](https://www.docker.com/products/docker-desktop/).

<br>

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51 changes: 40 additions & 11 deletions docs/index.html
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Expand Up @@ -479,6 +479,16 @@ <h1 class="title toc-ignore">VoltRon</h1>
<div style="width:70%; margin-left: auto; margin-right: auto">
<div style="float:left; margin-left: auto; margin-right: auto">
<p><br></p>
<div id="staying-up-to-date" class="section level2">
<h2>Staying up-to-date</h2>
<p>To ask questions please use VoltRon discussion forum on google
groups.</p>
<ul>
<li><a href="https://groups.google.com/forum/#!forum/voltron_discussion"
class="uri">https://groups.google.com/forum/#!forum/voltron_discussion</a></li>
</ul>
<p><br></p>
</div>
<div id="installation" class="section level2">
<h2>Installation</h2>
<p>Install from the GitHub repository using devtools (with R version
Expand All @@ -493,22 +503,41 @@ <h2>Installation</h2>
href="https://cran.r-project.org/bin/windows/Rtools/rtools43/rtools.html">Rtools</a>
may be required to be downloaded too, hence this may take some time!</p>
<p>On <strong>Ubuntu</strong> we provide a set of instructions that may
help users to build OpenCV with necessary headers <a
href="inst/extdata/install_ubuntu.md">here</a>.</p>
help users to build OpenCV with necessary headers [here](<a
href="https://github.com/BIMSBbioinfo/VoltRon/blob/main/inst/extdata/install_ubuntu.md"
class="uri">https://github.com/BIMSBbioinfo/VoltRon/blob/main/inst/extdata/install_ubuntu.md</a>.</p>
<p>On <strong>Fedora</strong> you may need <a
href="https://src.fedoraproject.org/rpms/opencv"><code>opencv-devel</code></a>:</p>
<pre class="sh"><code>yum install opencv-devel</code></pre>
<p><br></p>
</div>
<div id="tutorials" class="section level2">
<h2>Tutorials</h2>
<p>Please see the <a
href="https://artur-man.github.io/VoltRon/tutorials.html">Explore</a>
section in the VoltRon website for tutorials, example scripts and
analysis found in the <a
href="https://www.biorxiv.org/content/10.1101/2023.12.15.571667v1">preprint</a>.
Tutorials include links for accessing necessary data to run scripts
across all tutorials.</p>
<div id="dependencies" class="section level2">
<h2>Dependencies</h2>
<p>VoltRon incorporates <code>RBioformats</code> package to import
images from <code>ome.tiff</code> files, which requires <a
href="https://www.oracle.com/java/technologies/downloads/?er=221886">Java
JDK</a> to be available in your system:</p>
<p>See <a
href="https://cran.r-project.org/web/packages/rJava">https://cran.r-project.org/web/packages/rJava</a>
for more information.</p>
<p><br></p>
</div>
<div id="docker-hub" class="section level2">
<h2>Docker Hub</h2>
<p>You can also run VoltRon from a container already available in <a
href="https://hub.docker.com/repository/docker/amanukyan1385/rstudio-voltron/general">Docker
Hub</a>. The docker image is based on the <a
href="https://rocker-project.org/">Rocker Project</a> and can be run
from the terminal like below:</p>
<pre><code>docker run --rm -ti -e PASSWORD=&lt;yourpassword&gt; -p 8787:8787 amanukyan1385/rstudio-voltron:main</code></pre>
<p>Then, start the RStudio session from the browser at
<code>http://localhost:8787/</code> and enter <code>rstudio</code> as
username and <code>&lt;yourpassword&gt;</code> as password.</p>
<p>See <a
href="https://github.com/BIMSBbioinfo/VoltRon/blob/main/inst/extdata/docker_desktop_instructions.md">here</a>
for more instructions on how to run the container using <a
href="https://www.docker.com/products/docker-desktop/">Docker
Desktop</a>.</p>
<p><br></p>
</div>
<div id="references" class="section level2">
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