Merge branch 'quarto_roy'

NBISweden · Feb 5, 2024 · ebd3bed · ebd3bed
2 parents 94399b6 + f703acb
commit ebd3bed
Showing 1 changed file with 9 additions and 4 deletions.
diff --git 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" \
@@ -61,10 +64,12 @@ 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 -O /tmp/brain.tar.gz \
-    && Rscript -e 'install.packages("/tmp/brain.tar.gz", repos = NULL, type="source")' \
-    && rm -rf /tmp/brain.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/*
 rm -rf /tmp/downloaded_packages