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KellisLab · Jan 29, 2024 · 5ca2899 · 5ca2899
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commit 5ca2899
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Showing 2 changed files with 12 additions and 5 deletions.
diff --git a/R/installExtra.R b/R/installExtra.R
@@ -3,11 +3,18 @@
 installExtraPackages <- function(upgrade="never", seurat=TRUE, ...) {
 ### Reinstall seurat
     if (seurat) {
-        remotes::install_github("satijalab/seurat", "seurat5", upgrade=upgrade, ...)
+        remotes::install_github("satijalab/seurat-object", "v5.0.1", upgrade=upgrade, ...)
+        remotes::install_github("satijalab/seurat", "v5.0.1", upgrade=upgrade, ...)
         remotes::install_github("satijalab/seurat-data", "seurat5", upgrade=upgrade, ...)
         remotes::install_github("satijalab/seurat-wrappers", "seurat5", upgrade=upgrade, ...)
-        remotes::install_github("stuart-lab/signac", upgrade=upgrade, ...)
-        remotes::install_github("satijalab/azimuth", "seurat5", upgrade=upgrade, ...)
+        remotes::install_github("stuart-lab/signac", "1.12", upgrade=upgrade, ...)
+        tryCatch({
+            ### For some reason the github refs/branches do not work
+            remotes::install_github("satijalab/azimuth", "0.5.0", upgrade=upgrade, ...)
+        }, error=function(cond) {
+            print("Using bare Azimuth install")
+            remotes::install_github("satijalab/azimuth", upgrade=upgrade, ...)
+        })
     }
 ### Tools
     devtools::install_github('lhe17/nebula', upgrade=upgrade, ...)

diff --git a/conda/benj.yml.in b/conda/benj.yml.in
@@ -15,8 +15,8 @@ channels:
 
 dependencies:
   ## Must have
-  - conda-forge::anndata>=0.10.4
-  - conda-forge::scanpy>=1.9.6
+  - conda-forge::anndata>=0.10.5
+  - conda-forge::scanpy>=1.9.7
   - conda-forge::muon
   - conda-forge::pandas>=1.5.0
   - conda-forge::numpy>=1.21.6