Fix Seurat 5 container for SINCLAIR

seurat/seurat_5/Dockerfile.v1

@@ -19,8 +19,10 @@ RUN conda update -n base -c conda-forge conda && \
     echo "conda activate ${CONDA_ENV}" > ~/.bashrc && \
     chmod -R a+rx /opt2
 ENV PATH="/opt2/conda/envs/${CONDA_ENV}/bin:$PATH"
+ENV R_LIBS_USER="/opt2/conda/envs/${CONDA_ENV}/lib/R/library/"
 COPY install.R /data2/
-RUN Rscript /data2/install.R
+RUN Rscript /data2/install.R && \
+    R -s -e "readr::write_csv(tibble::as_tibble(installed.packages()), '/data2/r-packages.csv')"
 
 # Copy Dockerfile to container
 COPY ${DOCKERFILE} /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}

seurat/seurat_5/environment.yml

@@ -3,40 +3,53 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
+  - bioconductor-alabaster.base
   - bioconductor-annotationdbi
   - bioconductor-biocparallel
-  - bioconductor-celldex
   - bioconductor-genomeinfodbdata
   - bioconductor-glmgampoi
   - bioconductor-org.hs.eg.db
   - bioconductor-org.mm.eg.db
   - bioconductor-orthology.eg.db
   - bioconductor-scrnaseq
   - bioconductor-singlecellexperiment
-  - bioconductor-singler=2
-  - r-base=4
+  - bioconductor-singler
+  - bioconductor-celldex
+  - bioconductor-rhdf5
+  - bioconductor-assorthead
+  - r-base=4.4.3
   - r-cluster
   - r-cluster=2
   - r-cowplot
+  - r-dplyr
   - r-DT
   - r-essentials
   - r-evaluate>=1.0.3
   - r-farver
   - r-flexmix
+  - r-forcats
   - r-future.apply
+  - r-ggplot2=3
   - r-ggpubr
   - r-gridextra
-  - r-harmony=0.1
+  - r-harmony>=0.1
   - r-hdf5r
-  - r-liger=1
+  - r-httr2
+ # - r-r-liger
+  - r-lubridate
   - r-png
   - r-presto
+  - r-purrr
+  - r-readr
   - r-remotes
   - r-reticulate
   - r-r.utils
   - r-scales
-  - r-seurat=5.1
-  - r-signac=1
-  - r-tidyverse
+  - r-seurat=5.3
+  - r-signac
+  - r-stringr
+  - r-tibble
+  - r-tidyr
   - r-tinytex
   - scvi-tools=1.2
+  - zlib

seurat/seurat_5/install.R

@@ -1,7 +1,58 @@
 #!/usr/bin/env Rscript
 args <- commandArgs(trailingOnly = TRUE)
 setRepositories(ind = 1:3)
-remotes::install_github("satijalab/seurat-wrappers")
-remotes::install_github("chris-mcginnis-ucsf/DoubletFinder")
-remotes::install_github("mdelacre/Routliers")
-remotes::install_cran("BPCells", repos = c("https://bnprks.r-universe.dev"))
+
+remotes::install_cran(
+  "gypsum",
+  repos = "https://bioc.r-universe.dev/",
+  upgrade = "never"
+)
+remotes::install_cran("rliger", upgrade = "never")
+#remotes::install_bioc("rhdf5", upgrade = "never") 
+#remotes::install_bioc("assorthead", upgrade = "never")
+#remotes::install_bioc("alabaster.base", upgrade = "never")
+#remotes::install_bioc("celldex", upgrade = "never")
+
+remotes::install_github("satijalab/seurat-wrappers@73466e3", upgrade = "never")
+
+# https://github.com/chris-mcginnis-ucsf/DoubletFinder/issues/244
+remotes::install_github(
+  "chris-mcginnis-ucsf/DoubletFinder@aee4431",
+  upgrade = "never"
+) 
+
+remotes::install_version(
+  "Routliers",
+  repos = "https://cran.rstudio.com/",
+  version = "0.0.0.3",
+  upgrade = "never"
+)
+remotes::install_cran(
+  "BPCells",
+  repos = "https://bnprks.r-universe.dev",
+  upgrade = "never"
+)
+
+abort_packages_not_installed <- function(...) {
+  pkgs <- c(...)
+  package_status <- lapply(pkgs, rlang::is_installed) |> unlist()
+  names(package_status) <- pkgs
+  packages_not_installed <- Filter(isFALSE, package_status)
+  if (length(packages_not_installed) > 0) {
+    msg <- paste0(
+      "The following package(s) are required but are not installed: ",
+      paste0(names(packages_not_installed), collapse = ", ")
+    )
+    stop(msg)
+  }
+}
+
+abort_packages_not_installed(
+  'SeuratWrappers',
+  'DoubletFinder',
+  'Routliers',
+  'BPCells',
+  'gypsum',
+  'alabaster.base',
+  'celldex'
+)

seurat/seurat_5/v1-dev.README.md

@@ -1,9 +1,9 @@
 ## CCBR/Dockers2 nciccbr/seurat_5:v1-dev
 
-Dockerfile source: https://github.com/CCBR/Dockers2/blob/2cac85800ba3ba86fcc93ffc9ae360d03d1199d5/seurat/seurat_5/Dockerfile.v1
+Dockerfile source: https://github.com/CCBR/Dockers2/blob/7c5c4f081bda2bf7b62f95c0fe914ffbf60d0a15/seurat/seurat_5/Dockerfile.v1
 
 
-Built on: 2025-10-15_17:39:39 
+Built on: 2026-02-25_15:01:56 
 
 Build tag: v1-dev 
 
@@ -26,7 +26,7 @@ Dockerfile path in repo: seurat/seurat_5/Dockerfile.v1
 | fastQValidator | NOTINDOCKER |
 | fastqscreen | NOTINDOCKER |
 | git | 2.25.1 |
-| java | 2025-07-15 |
+| java | 1.8.0_422 |
 | kraken2 | NOTINDOCKER |
 | kronatools | NOTINDOCKER |
 | multiqc | NOTINDOCKER |
@@ -35,7 +35,7 @@ Dockerfile path in repo: seurat/seurat_5/Dockerfile.v1
 | pigz | 2.4 |
 | preseq | NOTINDOCKER |
 | python2 | 2.7.18 |
-| python3 | 3.13.8 |
+| python3 | 3.14.3 |
 | qualimap | NOTINDOCKER |
 | rsem | NOTINDOCKER |
 | rseqc | NOTINDOCKER |