From 619cb781df1e27018bbe8f8e4f1ba86324f1ddf2 Mon Sep 17 00:00:00 2001 From: Roy Francis Date: Mon, 5 Feb 2024 11:38:45 +0100 Subject: [PATCH] Added brain data into seurat spatial --- containers/scripts/install_seurat_spatial.sh | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/containers/scripts/install_seurat_spatial.sh b/containers/scripts/install_seurat_spatial.sh index 0575b122..a8f2b9c4 100755 --- a/containers/scripts/install_seurat_spatial.sh +++ b/containers/scripts/install_seurat_spatial.sh @@ -47,7 +47,10 @@ ln -sf \ install2.r --error --skipinstalled -n "$NCPUS" \ hdf5r \ umap \ - Seurat + remotes + +Rscript -e 'remotes::install_version("Seurat", "4.3.0"); + remotes::install_version("SeuratObject", "4.1.3");' ## Install packages with BiocManager (https://stackoverflow.com/a/62456026) installBioc.r --error --skipinstalled -n "$NCPUS" \ @@ -61,9 +64,11 @@ installGithub.r --update FALSE \ https://github.com/satijalab/seurat-data/tree/d6a8ce61ccb21a3b204f194d07009772c822791d ## Get brain data -wget seurat.nygenome.org/src/contrib/stxBrain.SeuratData_0.1.1.tar.gz \ - && R CMD INSTALL stxBrain.SeuratData_0.1.1.tar.gz \ - && rm -rf stxBrain.SeuratData_0.1.1.tar.gz +Rscript -e 'if (!("stxBrain.SeuratData" %in% rownames(SeuratData::InstalledData()))) InstallData("stxBrain")' + +#wget seurat.nygenome.org/src/contrib/stxBrain.SeuratData_0.1.1.tar.gz \ +# && R CMD INSTALL stxBrain.SeuratData_0.1.1.tar.gz \ +# && rm -rf stxBrain.SeuratData_0.1.1.tar.gz ## Clean up rm -rf /var/lib/apt/lists/*