Commit 03a1829a authored by Etienne Rifa's avatar Etienne Rifa
Browse files

v1.0.0

parent 42ffd5db
Package: ExploreMetabar
Title: ExploreMetabar
Version: 0.0.0.9000
Version: 1.0.0
Authors@R:
c(person(given = "Etienne",
family = "Rifa",
......
......@@ -187,6 +187,7 @@ merge_table <- function(rank, table){
#' @noRd
mod_data_loading_server <- function(input, output, session, r=r){
ns <- session$ns
cat(file=stderr(), '\n#############################\nRunning ExploreMetabar v1.0.0', "\n#############################\n\n")
r_values <- reactiveValues(phyobj_initial=NULL, phyobj_sub_samples=NULL, phyobj_norm=NULL, phyobj_taxglom=NULL, phyobj_final=NULL, phyobj_tmp=NULL)
......
<!-- README.md is generated from README.Rmd. Please edit that file -->
# ExploreMetabar
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4317188.svg)](https://doi.org/10.5281/zenodo.4317188)
<!-- badges: start -->
<!-- [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental) -->
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4317188.svg)](https://doi.org/10.5281/zenodo.4317188)
<!-- badges: end -->
ExploreMetabar is a shiny application used to explore metabarcoding data
(16S, ITS) with interactive plots, integrated statistical test, and
(16S, ITS) with interactive plots, integrated statistical tests, and
differential analysis.
## Online instance
ExploreMetabar is hosted on [migale bioinformatics facility](https://migale.inrae.fr/) and available at this link:
**[https://shiny.migale.inrae.fr/app/exploremetabar](https://shiny.migale.inrae.fr/app/exploremetabar)**
## Installation
R3.6.3 or upper is required.
* **Linux (recommended)**
On ubuntu 18.04 those libraries are needed:
```{r}
remotes::system_requirements(path = '.', os="ubuntu", os_release = "18.04")
[1] "apt-get install -y software-properties-common" "add-apt-repository -y ppa:cran/libgit2"
[3] "apt-get update" "apt-get install -y make"
[5] "apt-get install -y zlib1g-dev" "apt-get install -y libicu-dev"
[7] "apt-get install -y git" "apt-get install -y pandoc"
[9] "apt-get install -y libxml2-dev" "apt-get install -y libcurl4-openssl-dev"
[11] "apt-get install -y libssl-dev" "apt-get install -y libgit2-dev"
[13] "apt-get install -y libglpk-dev" "apt-get install -y libgmp3-dev"
[15] "apt-get install -y libjpeg-dev" "apt-get install -y libpng-dev"
```bash
apt-get update && apt-get install -y git-core libcurl4-openssl-dev libgit2-dev libglpk-dev libgmp-dev libicu-dev libpng-dev libssl-dev libxml2-dev make pandoc pandoc-citeproc zlib1g-dev libtiff-dev libjpeg-dev libbz2-dev libgmp3-dev software-properties-common
```
* Windows
R3.6.3 is required. For Windows, [Rtools](https://cran.r-project.org/bin/windows/Rtools/) and [git](https://git-scm.com/download/win) are required.
[Rtools](https://cran.r-project.org/bin/windows/Rtools/) and [git](https://git-scm.com/download/win) are required.
You can install the development version of ExploreMetabar from this
repository with:
......@@ -40,32 +40,28 @@ install.packages("devtools")
devtools::install_git("https://forgemia.inra.fr/umrf/exploremetabar")
```
## To run Shiny app
### To run Shiny app
``` r
library(ExploreMetabar)
ExploreMetabar::run_app()
```
## On ShinyApps.io
## Docker
To test ExploreMetabar:
https://erifa1.shinyapps.io/exploremetabar/ (old version)
To install ExploreMetabar via docker environment:
<!-- What is special about using `README.Rmd` instead of just `README.md`? You can include R chunks like so: -->
```bash
sudo docker pull erifa1/exploremetabar:v1.002
sudo docker run -it -p 3838:3838 erifa1/exploremetabar:v1.002
```
<!-- ```{r cars} -->
## Citation
<!-- summary(cars) -->
Etienne RIFA, & Sebastien Theil. (2020). ExploreMetabar: v1.0.0, https://forgemia.inra.fr/umrf/exploremetabar. Zenodo. https://doi.org/10.5281/zenodo.4317188
<!-- ``` -->
<!-- You'll still need to render `README.Rmd` regularly, to keep `README.md` up-to-date. -->
<!-- You can also embed plots, for example: -->
<!-- ```{r pressure, echo = FALSE} -->
<!-- plot(pressure) -->
<!-- ``` -->
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