From 93b06dc4769d5dddf9b5a6c4632778fad3a78a7e Mon Sep 17 00:00:00 2001
From: Triana <triana@embl.de>
Date: Sat, 24 Jul 2021 16:18:50 +0200
Subject: [PATCH] Solve Seurat compatibility to include 3.2.4
---
Dockerfile | 1 -
app/global.R | 1 -
packages.R | 27 +++++++--------------------
3 files changed, 7 insertions(+), 22 deletions(-)
diff --git a/Dockerfile b/Dockerfile
index 1f0ce5a..cddafef 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -10,5 +10,4 @@ ADD app/ /srv/shiny-server/
RUN Rscript packages.R
-RUN sed -i '2ienv | grep AWS > /home/shiny/.Renviron && chown shiny.shiny /home/shiny/.Renviron\n' /usr/bin/shiny-server.sh
diff --git a/app/global.R b/app/global.R
index 0e25a35..9a919cd 100644
--- a/app/global.R
+++ b/app/global.R
@@ -29,7 +29,6 @@ require(plotly)
require(shinycustomloader)
require(aws.s3)
require(future)
-require(shinyBS)
#require(minio.s3)
plan("multiprocess", workers = 4)
diff --git a/packages.R b/packages.R
index dd70439..2a5715b 100644
--- a/packages.R
+++ b/packages.R
@@ -1,32 +1,19 @@
-if (!requireNamespace("BiocManager", quietly = TRUE))
- install.packages("BiocManager")
-BiocManager::install("multtest")
-install.packages("metap")
-install.packages("mutoss")
-install.packages("BIOMOD", repos="http://R-Forge.R-project.org")
-install.packages("mclust")
+install.packages("remotes")
+remotes::install_version("rsvd", version = "1.0.3", repos = "http://cran.us.r-project.org")
+remove.packages(grep("spatstat", installed.packages(), value = T))
+remotes::install_version("spatstat", version = "1.64-1", repos = "http://cran.us.r-project.org",
+ upgrade = "never",force = T)
+remotes::install_version("Seurat", version = "3.2.3",repos = "http://cran.us.r-project.org",upgrade ="never" )
install.packages("devtools")
library(devtools)
devtools::install_github("thomasp85/patchwork")
-install.packages("plotly")
install.packages("shinycustomloader")
-install.packages("rpart")
-install.packages("rpart.plot")
install.packages("xml2")
install.packages("rgeos", repos="http://R-Forge.R-project.org", type="source")
-install.packages("ggplot2")
-install.packages("reshape2")
install.packages("plyr")
install.packages("gridExtra")
install.packages("waiter")
install.packages("grid")
install.packages("DT")
-install.packages("ggrepel")
-install.packages("RColorBrewer")
-install.packages("dplyr")
install.packages("future")
-##devtools::install_github(repo = 'satijalab/seurat', ref = 'develop')
-install.packages(c("sp", "polyclip"))
-if (!requireNamespace("BiocManager", quietly = TRUE))
- install.packages("BiocManager")
-remotes::install_version("Seurat", version = "3.2.3")
+install.packages("mclust")
--
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