From 007f8419e1cd5d48afe326335c1383e100817e68 Mon Sep 17 00:00:00 2001 From: Artur-man Date: Fri, 10 Jan 2025 00:03:54 +0100 Subject: [PATCH] update webpage intro and README --- README.md | 6 ++++++ docs/index.Rmd | 30 ++++++++++++++++++++++++++--- docs/index.html | 51 ++++++++++++++++++++++++++++++++++++++----------- 3 files changed, 73 insertions(+), 14 deletions(-) diff --git a/README.md b/README.md index e731c37..5252ede 100644 --- a/README.md +++ b/README.md @@ -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: diff --git a/docs/index.Rmd b/docs/index.Rmd index 1b41b83..5b33ea5 100644 --- a/docs/index.Rmd +++ b/docs/index.Rmd @@ -94,6 +94,14 @@ knitr::opts_chunk$set(echo = TRUE)
+## Staying up-to-date + +To ask questions please use VoltRon discussion forum on google groups. + +- https://groups.google.com/forum/#!forum/voltron_discussion + +
+ ## Installation Install from the GitHub repository using devtools (with R version 4.3.0 or higher): @@ -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): @@ -118,9 +126,25 @@ yum install opencv-devel
-## 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. + +
+ +## 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= -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 `` 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/).
diff --git a/docs/index.html b/docs/index.html index 411881b..1fc332b 100644 --- a/docs/index.html +++ b/docs/index.html @@ -479,6 +479,16 @@

VoltRon


+
+

Staying up-to-date

+

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

+ +


+

Installation

Install from the GitHub repository using devtools (with R version @@ -493,22 +503,41 @@

Installation

href="https://cran.r-project.org/bin/windows/Rtools/rtools43/rtools.html">Rtools 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.

+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:

yum install opencv-devel


-
-

Tutorials

-

Please see the Explore -section in the VoltRon website for tutorials, example scripts and -analysis found in the preprint. -Tutorials include links for accessing necessary data to run scripts -across all tutorials.

+
+

Dependencies

+

VoltRon incorporates RBioformats package to import +images from ome.tiff files, which requires Java +JDK to be available in your system:

+

See https://cran.r-project.org/web/packages/rJava +for more information.

+


+
+
+

Docker Hub

+

You can also run VoltRon from a container already available in Docker +Hub. The docker image is based on the Rocker Project 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.

+

See here +for more instructions on how to run the container using Docker +Desktop.