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The IDE needs a computer with an [R environment version >=3.5.0](https://www.r-project.org/) as well as a Java runtime environment version 8 or above. To compile R packages, C and FORTRAN compilers as well as a number of development libraries and tools are needed. It makes things easier if they are all installed system-wide in default locations using administrative privileges.
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##### For Linux
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1. Install Java using your system's package manager. On Debian derivatives (e.g. Ubuntu), run:
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1. Install Java using your system's package manager. On Debian derivatives (e.g. Ubuntu), open a terminal and run:
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```
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sudo apt install default-jre default-jdk
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The build-essential package contains the GNU compiler collection and various tools and development libraries that are required to build R packages.
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3. Install required system libraries.
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R packages used by the IDE require the following libraries: libssl, liblzma, libbz2, libicu, libtiff, libfftw3, libcurl4 with OpenSSL support, libxml2, libssh2-1 and libgit2. On Debian derivatives, run:
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R packages used by the IDE require the following libraries: libssl, liblzma, libbz2, libicu, libtiff, libfftw3, libcurl4 with OpenSSL support, libxml2, libssh2-1 and libgit2. On Debian derivatives, open a terminal and run:
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```
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sudo apt install libssl-dev liblzma-dev libbz2-dev libicu-dev libtiff-dev libfftw3-dev libcurl4-openssl-dev libxml2-dev libssh2-1-dev libgit2-dev
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![Download_Rtools_for_Windows.2](uploads/e3321268adec5c97897671ccaf753cd9/Download_Rtools_for_Windows.2.png)
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- Run the installer and select the default options.
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### R packages
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The IDE requires some R packages and will try to install them if it can't detect them on the system. In case of problems, it may be better to install the required packages manually. Note that package installation can take several minutes depending on how many dependencies are already present on the system.
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The IDE requires the following packages from CRAN: devtools, data.table, DT, shiny, shinyFiles, shinycssloaders, shinydashboard, shinyjs, shinyWidgets, shinybusy, assertthat, ggplot2, plotly, RANN, MASS, dbscan, uwot, xgboost, Ckmeans.1d.dp, e1071, caret, RColorBrewer, aws.s3.
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... | ... | @@ -92,15 +91,18 @@ The app is then accessible from a web browser (on the same machine the app was s |
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### Using RStudio
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1- [Download RStudio](https://www.rstudio.com/products/rstudio/download/#download). Install using your system installation procedure. If presented with options, choose default values.
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1- [Download RStudio](https://www.rstudio.com/products/rstudio/download/#download).
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![RStudio_downloads](uploads/6f700f477992c17a9326068a129d40a8/RStudio_downloads.png)
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Install using your system installation procedure. If presented with options, choose default values.
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2- Download the project's directory as a zip archive ([latest version](https://git.embl.de/heriche/image-data-explorer/-/archive/master/image-data-explorer-master.zip)) and unpack the archive.
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3- Start RStudio then:
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- navigate to the project's directory using RStudio's file browser
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- open the file image_data_explorer.R.
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- if RStudio asks to install missing packages, reply yes. Note: this can take several minutes depending on how many of the package dependencies have already been installed.
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- click the 'Run App' button. The app may install remaining missing packages then will open the IDE interface in a browser window.
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1. navigate to the project's directory using RStudio's file browser.
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2. open the file image_data_explorer.R.
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- if RStudio asks to install missing packages, reply yes. Note: this can take several minutes depending on how many of the package dependencies have already been installed.
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3. click the 'Run App' button. The app may install remaining missing packages then will open the IDE interface in a browser window. ![RStudio](uploads/2bf7fa5d03ec5b961dbcb58f1466ac52/RStudio.png)
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The app is accessible from a web browser (on the same machine RStudio is running on) at http://127.0.0.1:5476
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