From f4f4cb3b8d0815e52abcb43bd4013c89cd879772 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 15 Oct 2025 13:29:26 -0400
Subject: [PATCH 01/65] fix: add installation for non-conda R packages

---
 seurat/{sinclair_seurat_5 => seurat_5}/Dockerfile.v1     | 1 +
 seurat/{sinclair_seurat_5 => seurat_5}/environment.yml   | 0
 seurat/seurat_5/install.R                                | 7 +++++++
 seurat/{sinclair_seurat_5 => seurat_5}/v1-dev.README.md  | 0
 seurat/{sinclair_seurat_5 => seurat_5}/v1-feat.README.md | 0
 seurat/{sinclair_seurat_5 => seurat_5}/v1.README.md      | 0
 6 files changed, 8 insertions(+)
 rename seurat/{sinclair_seurat_5 => seurat_5}/Dockerfile.v1 (97%)
 rename seurat/{sinclair_seurat_5 => seurat_5}/environment.yml (100%)
 create mode 100644 seurat/seurat_5/install.R
 rename seurat/{sinclair_seurat_5 => seurat_5}/v1-dev.README.md (100%)
 rename seurat/{sinclair_seurat_5 => seurat_5}/v1-feat.README.md (100%)
 rename seurat/{sinclair_seurat_5 => seurat_5}/v1.README.md (100%)

diff --git a/seurat/sinclair_seurat_5/Dockerfile.v1 b/seurat/seurat_5/Dockerfile.v1
similarity index 97%
rename from seurat/sinclair_seurat_5/Dockerfile.v1
rename to seurat/seurat_5/Dockerfile.v1
index cad641d8..003b20bc 100644
--- a/seurat/sinclair_seurat_5/Dockerfile.v1
+++ b/seurat/seurat_5/Dockerfile.v1
@@ -18,6 +18,7 @@ RUN mamba env create -n ${CONDA_ENV} -f /data2/environment.yml && \
     echo "conda activate ${CONDA_ENV}" > ~/.bashrc && \
     chmod -R a+rx /opt2
 ENV PATH="/opt2/conda/envs/${CONDA_ENV}/bin:$PATH"
+RUN Rscript install.R
 
 # Copy Dockerfile to container
 COPY ${DOCKERFILE} /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
diff --git a/seurat/sinclair_seurat_5/environment.yml b/seurat/seurat_5/environment.yml
similarity index 100%
rename from seurat/sinclair_seurat_5/environment.yml
rename to seurat/seurat_5/environment.yml
diff --git a/seurat/seurat_5/install.R b/seurat/seurat_5/install.R
new file mode 100644
index 00000000..12446e13
--- /dev/null
+++ b/seurat/seurat_5/install.R
@@ -0,0 +1,7 @@
+#!/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"))
\ No newline at end of file
diff --git a/seurat/sinclair_seurat_5/v1-dev.README.md b/seurat/seurat_5/v1-dev.README.md
similarity index 100%
rename from seurat/sinclair_seurat_5/v1-dev.README.md
rename to seurat/seurat_5/v1-dev.README.md
diff --git a/seurat/sinclair_seurat_5/v1-feat.README.md b/seurat/seurat_5/v1-feat.README.md
similarity index 100%
rename from seurat/sinclair_seurat_5/v1-feat.README.md
rename to seurat/seurat_5/v1-feat.README.md
diff --git a/seurat/sinclair_seurat_5/v1.README.md b/seurat/seurat_5/v1.README.md
similarity index 100%
rename from seurat/sinclair_seurat_5/v1.README.md
rename to seurat/seurat_5/v1.README.md

From 8465b7fe608baf33ddf44c573535ab336f42925e Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 15 Oct 2025 13:38:38 -0400
Subject: [PATCH 02/65] fix: copy install script

---
 seurat/seurat_5/Dockerfile.v1 | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/seurat/seurat_5/Dockerfile.v1 b/seurat/seurat_5/Dockerfile.v1
index 003b20bc..a83c7955 100644
--- a/seurat/seurat_5/Dockerfile.v1
+++ b/seurat/seurat_5/Dockerfile.v1
@@ -14,11 +14,13 @@ ENV DOCKERFILE=${DOCKERFILE}
 # Specify all dependencies in environment.yml
 COPY environment.yml /data2/
 ENV CONDA_ENV=seurat5
-RUN mamba env create -n ${CONDA_ENV} -f /data2/environment.yml && \
+RUN conda update -n base -c conda-forge conda && \
+    mamba env create -n ${CONDA_ENV} -f /data2/environment.yml && \
     echo "conda activate ${CONDA_ENV}" > ~/.bashrc && \
     chmod -R a+rx /opt2
 ENV PATH="/opt2/conda/envs/${CONDA_ENV}/bin:$PATH"
-RUN Rscript install.R
+COPY install.R /data2/
+RUN Rscript /data2/install.R
 
 # Copy Dockerfile to container
 COPY ${DOCKERFILE} /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}

From 9a3f0bfb9ceefe2f6987742efcdab13fd07d3d8f Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 15 Oct 2025 14:59:00 -0400
Subject: [PATCH 03/65] fix: set R lib

---
 seurat/seurat_5/Dockerfile.v1 | 1 +
 1 file changed, 1 insertion(+)

diff --git a/seurat/seurat_5/Dockerfile.v1 b/seurat/seurat_5/Dockerfile.v1
index a83c7955..77782d6b 100644
--- a/seurat/seurat_5/Dockerfile.v1
+++ b/seurat/seurat_5/Dockerfile.v1
@@ -19,6 +19,7 @@ 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
 

From 77d091efcd548cc15fd1013fffce8e73439e5ef3 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 15 Oct 2025 14:59:08 -0400
Subject: [PATCH 04/65] fix: bump seurat to v5.3

---
 seurat/seurat_5/environment.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/seurat/seurat_5/environment.yml b/seurat/seurat_5/environment.yml
index 9b616c03..f42cf304 100644
--- a/seurat/seurat_5/environment.yml
+++ b/seurat/seurat_5/environment.yml
@@ -26,7 +26,7 @@ dependencies:
   - r-future.apply
   - r-ggpubr
   - r-gridextra
-  - r-harmony=0.1
+  - r-harmony>=0.1
   - r-hdf5r
   - r-liger=1
   - r-png
@@ -35,7 +35,7 @@ dependencies:
   - r-reticulate
   - r-r.utils
   - r-scales
-  - r-seurat=5.1
+  - r-seurat=5.3
   - r-signac=1
   - r-tidyverse
   - r-tinytex

From 0abbe5cae81b2af801a9cec42500e92d041ea26a Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Wed, 15 Oct 2025 19:25:21 +0000
Subject: [PATCH 05/65] =?UTF-8?q?docs:=20=F0=9F=A4=96=20update=20readme=20?=
 =?UTF-8?q?for=20seurat/seurat=5F5/Dockerfile.v1=20(#307)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: 41898282+github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 seurat/seurat_5/v1-dev.README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/seurat/seurat_5/v1-dev.README.md b/seurat/seurat_5/v1-dev.README.md
index 507786ea..cac3f6e4 100644
--- a/seurat/seurat_5/v1-dev.README.md
+++ b/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/73f9063a4089fde6438eb1f4043ffcf9b7ffb5ed/seurat/seurat_5/Dockerfile.v1
 
 
-Built on: 2025-10-15_17:39:39 
+Built on: 2025-10-15_19:01:10 
 
 Build tag: v1-dev 
 

From 61123fe522437e2947b2a9bd905915590eff4093 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 15 Oct 2025 15:34:10 -0400
Subject: [PATCH 06/65] feat: list R package versions

---
 seurat/seurat_5/Dockerfile.v1 | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/seurat/seurat_5/Dockerfile.v1 b/seurat/seurat_5/Dockerfile.v1
index 77782d6b..48da0311 100644
--- a/seurat/seurat_5/Dockerfile.v1
+++ b/seurat/seurat_5/Dockerfile.v1
@@ -21,7 +21,8 @@ RUN conda update -n base -c conda-forge conda && \
 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_tsv(tibble::as_tibble(installed.packages()), '/data2/r-packages.tsv')"
 
 # Copy Dockerfile to container
 COPY ${DOCKERFILE} /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}

From a17c133673fcd80af8787c34fe6d77ca231b9471 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Wed, 15 Oct 2025 19:59:41 +0000
Subject: [PATCH 07/65] =?UTF-8?q?docs:=20=F0=9F=A4=96=20update=20readme=20?=
 =?UTF-8?q?for=20seurat/seurat=5F5/Dockerfile.v1=20(#308)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: 41898282+github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 seurat/seurat_5/v1-dev.README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/seurat/seurat_5/v1-dev.README.md b/seurat/seurat_5/v1-dev.README.md
index cac3f6e4..fc043b9d 100644
--- a/seurat/seurat_5/v1-dev.README.md
+++ b/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/73f9063a4089fde6438eb1f4043ffcf9b7ffb5ed/seurat/seurat_5/Dockerfile.v1
+Dockerfile source: https://github.com/CCBR/Dockers2/blob/4bb235f7f81c36841ab33d2975246c8b07bf04c5/seurat/seurat_5/Dockerfile.v1
 
 
-Built on: 2025-10-15_19:01:10 
+Built on: 2025-10-15_19:36:04 
 
 Build tag: v1-dev 
 

From 76f3994f598dade7799d564cc1940990617752c9 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 15 Oct 2025 16:04:34 -0400
Subject: [PATCH 08/65] fix: specify R ggplot2 < 4.0.0

---
 seurat/seurat_5/environment.yml | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/seurat/seurat_5/environment.yml b/seurat/seurat_5/environment.yml
index f42cf304..ed025faa 100644
--- a/seurat/seurat_5/environment.yml
+++ b/seurat/seurat_5/environment.yml
@@ -18,25 +18,33 @@ dependencies:
   - 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<4
   - r-ggpubr
   - r-gridextra
   - r-harmony>=0.1
   - r-hdf5r
   - r-liger=1
+  - r-lubridate
   - r-png
   - r-presto
+  - r-purrr
+  - r-readr
   - r-remotes
   - r-reticulate
   - r-r.utils
   - r-scales
   - r-seurat=5.3
   - r-signac=1
-  - r-tidyverse
+  - r-stringr
+  - r-tibble
+  - r-tidyr
   - r-tinytex
   - scvi-tools=1.2

From 14c4e2921c82d69d028ba17b6e5cc6dd2e419589 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Wed, 15 Oct 2025 20:29:36 +0000
Subject: [PATCH 09/65] =?UTF-8?q?docs:=20=F0=9F=A4=96=20update=20readme=20?=
 =?UTF-8?q?for=20seurat/seurat=5F5/Dockerfile.v1=20(#309)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: 41898282+github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 seurat/seurat_5/v1-dev.README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/seurat/seurat_5/v1-dev.README.md b/seurat/seurat_5/v1-dev.README.md
index fc043b9d..9a70f84f 100644
--- a/seurat/seurat_5/v1-dev.README.md
+++ b/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/4bb235f7f81c36841ab33d2975246c8b07bf04c5/seurat/seurat_5/Dockerfile.v1
+Dockerfile source: https://github.com/CCBR/Dockers2/blob/442ca29331561bf6f3d92ac96d95a5d20a815595/seurat/seurat_5/Dockerfile.v1
 
 
-Built on: 2025-10-15_19:36:04 
+Built on: 2025-10-15_20:06:21 
 
 Build tag: v1-dev 
 

From 8bf63455b63c029030892725a35e288803411c61 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 15 Oct 2025 17:21:48 -0400
Subject: [PATCH 10/65] fix: specify ggplot2=3

---
 seurat/seurat_5/environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/seurat/seurat_5/environment.yml b/seurat/seurat_5/environment.yml
index ed025faa..ddd26bc8 100644
--- a/seurat/seurat_5/environment.yml
+++ b/seurat/seurat_5/environment.yml
@@ -26,7 +26,7 @@ dependencies:
   - r-flexmix
   - r-forcats
   - r-future.apply
-  - r-ggplot2<4
+  - r-ggplot2=3
   - r-ggpubr
   - r-gridextra
   - r-harmony>=0.1

From a300cacab0e676be9ad01c83edf107ba1b1c3ddd Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Wed, 15 Oct 2025 21:47:57 +0000
Subject: [PATCH 11/65] =?UTF-8?q?docs:=20=F0=9F=A4=96=20update=20readme=20?=
 =?UTF-8?q?for=20seurat/seurat=5F5/Dockerfile.v1=20(#310)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: 41898282+github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 seurat/seurat_5/v1-dev.README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/seurat/seurat_5/v1-dev.README.md b/seurat/seurat_5/v1-dev.README.md
index 9a70f84f..308e5091 100644
--- a/seurat/seurat_5/v1-dev.README.md
+++ b/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/442ca29331561bf6f3d92ac96d95a5d20a815595/seurat/seurat_5/Dockerfile.v1
+Dockerfile source: https://github.com/CCBR/Dockers2/blob/6bd0cef865e6341b61aa2b2d81bc6892462e070f/seurat/seurat_5/Dockerfile.v1
 
 
-Built on: 2025-10-15_20:06:21 
+Built on: 2025-10-15_21:24:02 
 
 Build tag: v1-dev 
 

From 8ec3baf42eb20288c4fa3f379348e5db0a0d6ae2 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Thu, 16 Oct 2025 09:33:48 -0400
Subject: [PATCH 12/65] fix: upgrade="never"

---
 seurat/seurat_5/install.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/seurat/seurat_5/install.R b/seurat/seurat_5/install.R
index 12446e13..22ce275e 100644
--- a/seurat/seurat_5/install.R
+++ b/seurat/seurat_5/install.R
@@ -1,7 +1,7 @@
 #!/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"))
\ No newline at end of file
+remotes::install_github("satijalab/seurat-wrappers", upgrade = "never")
+remotes::install_github("chris-mcginnis-ucsf/DoubletFinder", upgrade = "never")
+remotes::install_version("mdelacre/Routliers", version = "0.0.0.3", upgrade = "never")
+remotes::install_cran("BPCells", repos = c("https://bnprks.r-universe.dev"), upgrade = "never")
\ No newline at end of file

From 9646bbfa8cebd44b000d6e1f3e4ffc0e654c8828 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Thu, 16 Oct 2025 09:34:07 -0400
Subject: [PATCH 13/65] fix: Routliers is on CRAN

---
 seurat/seurat_5/install.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/seurat/seurat_5/install.R b/seurat/seurat_5/install.R
index 22ce275e..f4c59d65 100644
--- a/seurat/seurat_5/install.R
+++ b/seurat/seurat_5/install.R
@@ -3,5 +3,5 @@ args <- commandArgs(trailingOnly = TRUE)
 setRepositories(ind = 1:3)
 remotes::install_github("satijalab/seurat-wrappers", upgrade = "never")
 remotes::install_github("chris-mcginnis-ucsf/DoubletFinder", upgrade = "never")
-remotes::install_version("mdelacre/Routliers", version = "0.0.0.3", upgrade = "never")
+remotes::install_version("Routliers", version = "0.0.0.3", upgrade = "never")
 remotes::install_cran("BPCells", repos = c("https://bnprks.r-universe.dev"), upgrade = "never")
\ No newline at end of file

From d6d9cbf38412c9e51d4fd876dceddb7345eae131 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Thu, 16 Oct 2025 10:05:26 -0400
Subject: [PATCH 14/65] fix: explicitly set cran repo

---
 seurat/seurat_5/install.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/seurat/seurat_5/install.R b/seurat/seurat_5/install.R
index f4c59d65..413835b1 100644
--- a/seurat/seurat_5/install.R
+++ b/seurat/seurat_5/install.R
@@ -3,5 +3,5 @@ args <- commandArgs(trailingOnly = TRUE)
 setRepositories(ind = 1:3)
 remotes::install_github("satijalab/seurat-wrappers", upgrade = "never")
 remotes::install_github("chris-mcginnis-ucsf/DoubletFinder", upgrade = "never")
-remotes::install_version("Routliers", version = "0.0.0.3", upgrade = "never")
+remotes::install_version("Routliers", repos = c("https://cran.rstudio.com/"), version = "0.0.0.3", upgrade = "never")
 remotes::install_cran("BPCells", repos = c("https://bnprks.r-universe.dev"), upgrade = "never")
\ No newline at end of file

From 5261c3c86f47adf7f5024ab9818139adc2dccf75 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Thu, 16 Oct 2025 14:21:07 +0000
Subject: [PATCH 15/65] =?UTF-8?q?docs:=20=F0=9F=A4=96=20update=20readme=20?=
 =?UTF-8?q?for=20seurat/seurat=5F5/Dockerfile.v1=20(#312)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: 41898282+github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 seurat/seurat_5/v1-dev.README.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/seurat/seurat_5/v1-dev.README.md b/seurat/seurat_5/v1-dev.README.md
index 308e5091..03b37067 100644
--- a/seurat/seurat_5/v1-dev.README.md
+++ b/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/6bd0cef865e6341b61aa2b2d81bc6892462e070f/seurat/seurat_5/Dockerfile.v1
+Dockerfile source: https://github.com/CCBR/Dockers2/blob/af72ad2f272b33bf50edac3b24f0cce83dfaa43d/seurat/seurat_5/Dockerfile.v1
 
 
-Built on: 2025-10-15_21:24:02 
+Built on: 2025-10-16_14:06:26 
 
 Build tag: v1-dev 
 
@@ -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 | 3.13.9 |
 | qualimap | NOTINDOCKER |
 | rsem | NOTINDOCKER |
 | rseqc | NOTINDOCKER |

From f536fb013258aed8b65d25101d9ec7b1c7bfab40 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Thu, 16 Oct 2025 11:47:06 -0400
Subject: [PATCH 16/65] fix: install gypsum

---
 seurat/seurat_5/environment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/seurat/seurat_5/environment.yml b/seurat/seurat_5/environment.yml
index ddd26bc8..96822e5b 100644
--- a/seurat/seurat_5/environment.yml
+++ b/seurat/seurat_5/environment.yml
@@ -8,6 +8,7 @@ dependencies:
   - bioconductor-celldex
   - bioconductor-genomeinfodbdata
   - bioconductor-glmgampoi
+  - bioconductor-gypsum
   - bioconductor-org.hs.eg.db
   - bioconductor-org.mm.eg.db
   - bioconductor-orthology.eg.db

From 7badf40a5920da89a82c1cb87748561d5351b13f Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Thu, 16 Oct 2025 12:48:54 -0400
Subject: [PATCH 17/65] fix: specify gypsum <= 1.2

---
 seurat/seurat_5/environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/seurat/seurat_5/environment.yml b/seurat/seurat_5/environment.yml
index 96822e5b..b182457f 100644
--- a/seurat/seurat_5/environment.yml
+++ b/seurat/seurat_5/environment.yml
@@ -8,7 +8,7 @@ dependencies:
   - bioconductor-celldex
   - bioconductor-genomeinfodbdata
   - bioconductor-glmgampoi
-  - bioconductor-gypsum
+  - bioconductor-gypsum<=1.2
   - bioconductor-org.hs.eg.db
   - bioconductor-org.mm.eg.db
   - bioconductor-orthology.eg.db

From fe9524fd9978c529352b3a419db8389c6bd74654 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Thu, 16 Oct 2025 13:21:41 -0400
Subject: [PATCH 18/65] fix: do not restrict liger version

---
 seurat/seurat_5/environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/seurat/seurat_5/environment.yml b/seurat/seurat_5/environment.yml
index b182457f..0953091a 100644
--- a/seurat/seurat_5/environment.yml
+++ b/seurat/seurat_5/environment.yml
@@ -32,7 +32,7 @@ dependencies:
   - r-gridextra
   - r-harmony>=0.1
   - r-hdf5r
-  - r-liger=1
+  - r-liger
   - r-lubridate
   - r-png
   - r-presto

From 77b6cf34755d7c4bb286bc2825cd8258e46b93fb Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Thu, 16 Oct 2025 13:37:53 -0400
Subject: [PATCH 19/65] fix: try installing gypsum from R universe

---
 seurat/seurat_5/environment.yml | 1 -
 seurat/seurat_5/install.R       | 3 ++-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/seurat/seurat_5/environment.yml b/seurat/seurat_5/environment.yml
index 0953091a..078c9165 100644
--- a/seurat/seurat_5/environment.yml
+++ b/seurat/seurat_5/environment.yml
@@ -8,7 +8,6 @@ dependencies:
   - bioconductor-celldex
   - bioconductor-genomeinfodbdata
   - bioconductor-glmgampoi
-  - bioconductor-gypsum<=1.2
   - bioconductor-org.hs.eg.db
   - bioconductor-org.mm.eg.db
   - bioconductor-orthology.eg.db
diff --git a/seurat/seurat_5/install.R b/seurat/seurat_5/install.R
index 413835b1..315820ec 100644
--- a/seurat/seurat_5/install.R
+++ b/seurat/seurat_5/install.R
@@ -4,4 +4,5 @@ setRepositories(ind = 1:3)
 remotes::install_github("satijalab/seurat-wrappers", upgrade = "never")
 remotes::install_github("chris-mcginnis-ucsf/DoubletFinder", upgrade = "never")
 remotes::install_version("Routliers", repos = c("https://cran.rstudio.com/"), version = "0.0.0.3", upgrade = "never")
-remotes::install_cran("BPCells", repos = c("https://bnprks.r-universe.dev"), upgrade = "never")
\ No newline at end of file
+remotes::install_cran("BPCells", repos = c("https://bnprks.r-universe.dev"), upgrade = "never")
+remotes::install_cran('gypsum', repos = 'https://bioc.r-universe.dev/', upgrade = "never")
\ No newline at end of file

From 2d693f07decd67aa3b6ae4d989c427880a1c1cdc Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Thu, 16 Oct 2025 13:38:29 -0400
Subject: [PATCH 20/65] fix: liger v1 is required

---
 seurat/seurat_5/environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/seurat/seurat_5/environment.yml b/seurat/seurat_5/environment.yml
index 078c9165..ddd26bc8 100644
--- a/seurat/seurat_5/environment.yml
+++ b/seurat/seurat_5/environment.yml
@@ -31,7 +31,7 @@ dependencies:
   - r-gridextra
   - r-harmony>=0.1
   - r-hdf5r
-  - r-liger
+  - r-liger=1
   - r-lubridate
   - r-png
   - r-presto

From 05db26e5d553ce3c6b77ead667334b195432315f Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Thu, 16 Oct 2025 17:54:29 +0000
Subject: [PATCH 21/65] =?UTF-8?q?docs:=20=F0=9F=A4=96=20update=20readme=20?=
 =?UTF-8?q?for=20seurat/seurat=5F5/Dockerfile.v1=20(#313)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: 41898282+github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 seurat/seurat_5/v1-dev.README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/seurat/seurat_5/v1-dev.README.md b/seurat/seurat_5/v1-dev.README.md
index 03b37067..c8cf55d8 100644
--- a/seurat/seurat_5/v1-dev.README.md
+++ b/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/af72ad2f272b33bf50edac3b24f0cce83dfaa43d/seurat/seurat_5/Dockerfile.v1
+Dockerfile source: https://github.com/CCBR/Dockers2/blob/543b14f60f872121c4ee40534f167a462d410887/seurat/seurat_5/Dockerfile.v1
 
 
-Built on: 2025-10-16_14:06:26 
+Built on: 2025-10-16_17:39:32 
 
 Build tag: v1-dev 
 

From 5ee69230b4329e576831d88fe17f871aabdf7bd4 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Fri, 24 Oct 2025 14:41:08 -0400
Subject: [PATCH 22/65] fix: gypsum deps

---
 seurat/seurat_5/environment.yml | 2 ++
 seurat/seurat_5/install.R       | 6 +++---
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/seurat/seurat_5/environment.yml b/seurat/seurat_5/environment.yml
index ddd26bc8..d513ebb4 100644
--- a/seurat/seurat_5/environment.yml
+++ b/seurat/seurat_5/environment.yml
@@ -31,6 +31,7 @@ dependencies:
   - r-gridextra
   - r-harmony>=0.1
   - r-hdf5r
+  - r-httr2
   - r-liger=1
   - r-lubridate
   - r-png
@@ -48,3 +49,4 @@ dependencies:
   - r-tidyr
   - r-tinytex
   - scvi-tools=1.2
+  - zlib
\ No newline at end of file
diff --git a/seurat/seurat_5/install.R b/seurat/seurat_5/install.R
index 315820ec..c78d71fe 100644
--- a/seurat/seurat_5/install.R
+++ b/seurat/seurat_5/install.R
@@ -3,6 +3,6 @@ args <- commandArgs(trailingOnly = TRUE)
 setRepositories(ind = 1:3)
 remotes::install_github("satijalab/seurat-wrappers", upgrade = "never")
 remotes::install_github("chris-mcginnis-ucsf/DoubletFinder", upgrade = "never")
-remotes::install_version("Routliers", repos = c("https://cran.rstudio.com/"), version = "0.0.0.3", upgrade = "never")
-remotes::install_cran("BPCells", repos = c("https://bnprks.r-universe.dev"), upgrade = "never")
-remotes::install_cran('gypsum', repos = 'https://bioc.r-universe.dev/', upgrade = "never")
\ No newline at end of file
+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")
+remotes::install_cran("gypsum", repos = "https://bioc.r-universe.dev/", upgrade = "never")
\ No newline at end of file

From 832adb72df2b0636bda7d29316aa0d1f27b40732 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Fri, 24 Oct 2025 19:04:04 +0000
Subject: [PATCH 23/65] =?UTF-8?q?docs:=20=F0=9F=A4=96=20update=20readme=20?=
 =?UTF-8?q?for=20seurat/seurat=5F5/Dockerfile.v1=20(#314)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: 41898282+github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 seurat/seurat_5/v1-dev.README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/seurat/seurat_5/v1-dev.README.md b/seurat/seurat_5/v1-dev.README.md
index c8cf55d8..2d4c481c 100644
--- a/seurat/seurat_5/v1-dev.README.md
+++ b/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/543b14f60f872121c4ee40534f167a462d410887/seurat/seurat_5/Dockerfile.v1
+Dockerfile source: https://github.com/CCBR/Dockers2/blob/2b54997b67ed47f44645a6fb819509bb922ebab8/seurat/seurat_5/Dockerfile.v1
 
 
-Built on: 2025-10-16_17:39:32 
+Built on: 2025-10-24_18:43:08 
 
 Build tag: v1-dev 
 

From 10d18c721e5e6ee2b10d8fea0b564ac9d2120c8f Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Fri, 7 Nov 2025 10:11:39 -0500
Subject: [PATCH 24/65] fix: install DoubletFinder v2.0.4

see https://github.com/chris-mcginnis-ucsf/DoubletFinder/issues/244
---
 seurat/seurat_5/install.R | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/seurat/seurat_5/install.R b/seurat/seurat_5/install.R
index c78d71fe..48b59d73 100644
--- a/seurat/seurat_5/install.R
+++ b/seurat/seurat_5/install.R
@@ -2,7 +2,10 @@
 args <- commandArgs(trailingOnly = TRUE)
 setRepositories(ind = 1:3)
 remotes::install_github("satijalab/seurat-wrappers", upgrade = "never")
-remotes::install_github("chris-mcginnis-ucsf/DoubletFinder", upgrade = "never")
+
+# https://github.com/chris-mcginnis-ucsf/DoubletFinder/issues/244
+remotes::install_github("chris-mcginnis-ucsf/DoubletFinder@3b420df", 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")
 remotes::install_cran("gypsum", repos = "https://bioc.r-universe.dev/", upgrade = "never")
\ No newline at end of file

From aeced77471328967ad6a9c9d7eab3943901e3943 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Fri, 7 Nov 2025 15:33:32 +0000
Subject: [PATCH 25/65] =?UTF-8?q?docs:=20=F0=9F=A4=96=20update=20readme=20?=
 =?UTF-8?q?for=20seurat/seurat=5F5/Dockerfile.v1=20(#316)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: 41898282+github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 seurat/seurat_5/v1-dev.README.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/seurat/seurat_5/v1-dev.README.md b/seurat/seurat_5/v1-dev.README.md
index 2d4c481c..3f8f85b9 100644
--- a/seurat/seurat_5/v1-dev.README.md
+++ b/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/2b54997b67ed47f44645a6fb819509bb922ebab8/seurat/seurat_5/Dockerfile.v1
+Dockerfile source: https://github.com/CCBR/Dockers2/blob/b699ecb88f02a2a667912ec6f2d7ed6288a6399d/seurat/seurat_5/Dockerfile.v1
 
 
-Built on: 2025-10-24_18:43:08 
+Built on: 2025-11-07_15:12:49 
 
 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 | 2025-10-21 |
 | kraken2 | NOTINDOCKER |
 | kronatools | NOTINDOCKER |
 | multiqc | NOTINDOCKER |

From 5e01767f6d0b3cc81cc184be888a5f7fe563fef3 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Fri, 7 Nov 2025 15:55:28 +0000
Subject: [PATCH 26/65] =?UTF-8?q?docs:=20=F0=9F=A4=96=20update=20readme=20?=
 =?UTF-8?q?for=20seurat/seurat=5F5/Dockerfile.v1=20(#317)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: 41898282+github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 seurat/seurat_5/v1-dev.README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/seurat/seurat_5/v1-dev.README.md b/seurat/seurat_5/v1-dev.README.md
index 3f8f85b9..af0d1aa0 100644
--- a/seurat/seurat_5/v1-dev.README.md
+++ b/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/b699ecb88f02a2a667912ec6f2d7ed6288a6399d/seurat/seurat_5/Dockerfile.v1
+Dockerfile source: https://github.com/CCBR/Dockers2/blob/1e3e6531d212be68713207096daf72732906887d/seurat/seurat_5/Dockerfile.v1
 
 
-Built on: 2025-11-07_15:12:49 
+Built on: 2025-11-07_15:35:27 
 
 Build tag: v1-dev 
 

From 1946e9f85ec75e857d3b196a2ea898a352333a0a Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Fri, 7 Nov 2025 15:25:52 -0500
Subject: [PATCH 27/65] fix: set DoubletFinder commit hash from R lib dir on
 biowulf

---
 seurat/seurat_5/install.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/seurat/seurat_5/install.R b/seurat/seurat_5/install.R
index 48b59d73..c7f9d381 100644
--- a/seurat/seurat_5/install.R
+++ b/seurat/seurat_5/install.R
@@ -4,7 +4,7 @@ setRepositories(ind = 1:3)
 remotes::install_github("satijalab/seurat-wrappers", upgrade = "never")
 
 # https://github.com/chris-mcginnis-ucsf/DoubletFinder/issues/244
-remotes::install_github("chris-mcginnis-ucsf/DoubletFinder@3b420df", upgrade = "never")
+remotes::install_github("chris-mcginnis-ucsf/DoubletFinder@67fb8b5", 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")

From 15ef6ef25786c0e5ac21947ee4e333cbdcbeefee Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Fri, 7 Nov 2025 20:48:00 +0000
Subject: [PATCH 28/65] =?UTF-8?q?docs:=20=F0=9F=A4=96=20update=20readme=20?=
 =?UTF-8?q?for=20seurat/seurat=5F5/Dockerfile.v1=20(#318)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: 41898282+github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 seurat/seurat_5/v1-dev.README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/seurat/seurat_5/v1-dev.README.md b/seurat/seurat_5/v1-dev.README.md
index af0d1aa0..fc66d7ee 100644
--- a/seurat/seurat_5/v1-dev.README.md
+++ b/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/1e3e6531d212be68713207096daf72732906887d/seurat/seurat_5/Dockerfile.v1
+Dockerfile source: https://github.com/CCBR/Dockers2/blob/7c291ec365f14e39316351d794d5aa825fb89baf/seurat/seurat_5/Dockerfile.v1
 
 
-Built on: 2025-11-07_15:35:27 
+Built on: 2025-11-07_20:26:59 
 
 Build tag: v1-dev 
 

From 4d86a6e5517257ea701802d90793323fede31056 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Fri, 7 Nov 2025 16:05:49 -0500
Subject: [PATCH 29/65] fix: throw error if packages are not installed

---
 seurat/seurat_5/install.R | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/seurat/seurat_5/install.R b/seurat/seurat_5/install.R
index c7f9d381..0cdbc246 100644
--- a/seurat/seurat_5/install.R
+++ b/seurat/seurat_5/install.R
@@ -1,11 +1,25 @@
 #!/usr/bin/env Rscript
 args <- commandArgs(trailingOnly = TRUE)
 setRepositories(ind = 1:3)
-remotes::install_github("satijalab/seurat-wrappers", 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@67fb8b5", 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")
-remotes::install_cran("gypsum", repos = "https://bioc.r-universe.dev/", upgrade = "never")
\ No newline at end of file
+remotes::install_cran("gypsum", repos = "https://bioc.r-universe.dev/", upgrade = "never")
+
+abort_packages_not_installed <- function(...) {
+  package_status <- lapply(c(...), rlang::is_installed)
+  packages_not_installed <- Filter(isFALSE, package_status) |> unlist()
+  if (length(packages_not_installed) > 0) {
+    msg <- paste0(
+      "The following package(s) are required but are not installed: \n  ",
+      paste0(names(packages_not_installed), collapse = ", ")
+    )
+    stop(msg)
+  }
+}
+
+abort_packages_not_installed('SeuratWrappers', 'DoubletFinder', 'Routliers', 'BPCells', 'gypsum')

From 4ec8c2a857c5b62243915d04228920e2520b1600 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Fri, 7 Nov 2025 21:27:54 +0000
Subject: [PATCH 30/65] =?UTF-8?q?docs:=20=F0=9F=A4=96=20update=20readme=20?=
 =?UTF-8?q?for=20seurat/seurat=5F5/Dockerfile.v1=20(#319)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: 41898282+github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 seurat/seurat_5/v1-dev.README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/seurat/seurat_5/v1-dev.README.md b/seurat/seurat_5/v1-dev.README.md
index fc66d7ee..32371b98 100644
--- a/seurat/seurat_5/v1-dev.README.md
+++ b/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/7c291ec365f14e39316351d794d5aa825fb89baf/seurat/seurat_5/Dockerfile.v1
+Dockerfile source: https://github.com/CCBR/Dockers2/blob/d2ad5a463d24824de986ff943146760be586f3ac/seurat/seurat_5/Dockerfile.v1
 
 
-Built on: 2025-11-07_20:26:59 
+Built on: 2025-11-07_21:07:00 
 
 Build tag: v1-dev 
 

From b5cd80b3f193785435250333f94bd9d49798c7dd Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Mon, 10 Nov 2025 15:53:58 -0500
Subject: [PATCH 31/65] fix: switch to later commit of DoubletFinder

---
 seurat/seurat_5/install.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/seurat/seurat_5/install.R b/seurat/seurat_5/install.R
index 0cdbc246..153c8e72 100644
--- a/seurat/seurat_5/install.R
+++ b/seurat/seurat_5/install.R
@@ -4,7 +4,7 @@ setRepositories(ind = 1:3)
 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@67fb8b5", upgrade = "never")
+remotes::install_github("chris-mcginnis-ucsf/DoubletFinder@3b420df", 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")

From 40bd9d29fbacc5349245c6529cdd9d10d7974cc1 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Mon, 10 Nov 2025 21:16:11 +0000
Subject: [PATCH 32/65] =?UTF-8?q?docs:=20=F0=9F=A4=96=20update=20readme=20?=
 =?UTF-8?q?for=20seurat/seurat=5F5/Dockerfile.v1=20(#320)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: 41898282+github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 seurat/seurat_5/v1-dev.README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/seurat/seurat_5/v1-dev.README.md b/seurat/seurat_5/v1-dev.README.md
index 32371b98..3a809251 100644
--- a/seurat/seurat_5/v1-dev.README.md
+++ b/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/d2ad5a463d24824de986ff943146760be586f3ac/seurat/seurat_5/Dockerfile.v1
+Dockerfile source: https://github.com/CCBR/Dockers2/blob/b238a7797ca293c2e7bce225fb0a98d31ec2b121/seurat/seurat_5/Dockerfile.v1
 
 
-Built on: 2025-11-07_21:07:00 
+Built on: 2025-11-10_20:55:00 
 
 Build tag: v1-dev 
 

From 5e288ec0d5821512721f30e73e6d6384a4ceba71 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 19 Nov 2025 14:14:32 -0500
Subject: [PATCH 33/65] fix: set versions based on old R package config from
 sinclair

https://github.com/CCBR/SINCLAIR/blob/115c5fa3c5f386113b3bdd2488e0d14ab5dc47e0/conf/Rpack.config
---
 seurat/seurat_5/environment.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/seurat/seurat_5/environment.yml b/seurat/seurat_5/environment.yml
index d513ebb4..444e6013 100644
--- a/seurat/seurat_5/environment.yml
+++ b/seurat/seurat_5/environment.yml
@@ -3,16 +3,16 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconductor-annotationdbi
+  - bioconductor-annotationdbi=1.62.2
   - bioconductor-biocparallel
-  - bioconductor-celldex
+  - bioconductor-celldex>=1.20.0
   - bioconductor-genomeinfodbdata
   - bioconductor-glmgampoi
   - bioconductor-org.hs.eg.db
   - bioconductor-org.mm.eg.db
-  - bioconductor-orthology.eg.db
-  - bioconductor-scrnaseq
-  - bioconductor-singlecellexperiment
+  - bioconductor-orthology.eg.db=3.17.0
+  - bioconductor-scrnaseq=2.14.0
+  - bioconductor-singlecellexperiment=1.22.0
   - bioconductor-singler=2
   - r-base=4
   - r-cluster

From 7894a5c18adb054bb89caba086b24bde5af8f5b2 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 19 Nov 2025 14:30:08 -0500
Subject: [PATCH 34/65] fix: downgrade celldex to 1.16

https://anaconda.org/bioconda/bioconductor-celldex
---
 seurat/seurat_5/environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/seurat/seurat_5/environment.yml b/seurat/seurat_5/environment.yml
index 444e6013..87a24bf8 100644
--- a/seurat/seurat_5/environment.yml
+++ b/seurat/seurat_5/environment.yml
@@ -5,7 +5,7 @@ channels:
 dependencies:
   - bioconductor-annotationdbi=1.62.2
   - bioconductor-biocparallel
-  - bioconductor-celldex>=1.20.0
+  - bioconductor-celldex>=1.16.0
   - bioconductor-genomeinfodbdata
   - bioconductor-glmgampoi
   - bioconductor-org.hs.eg.db

From dda0c42e446218e140c5fba8166aaff24efbcb73 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 19 Nov 2025 14:50:20 -0500
Subject: [PATCH 35/65] fix: drop annotationdbi version

---
 seurat/seurat_5/environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/seurat/seurat_5/environment.yml b/seurat/seurat_5/environment.yml
index 87a24bf8..a724b70b 100644
--- a/seurat/seurat_5/environment.yml
+++ b/seurat/seurat_5/environment.yml
@@ -3,7 +3,7 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconductor-annotationdbi=1.62.2
+  - bioconductor-annotationdbi
   - bioconductor-biocparallel
   - bioconductor-celldex>=1.16.0
   - bioconductor-genomeinfodbdata

From 0808a4750fc336e6db83e153cc50d5af38f0c8de Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 19 Nov 2025 17:25:48 -0500
Subject: [PATCH 36/65] fix: install celldex via remotes

---
 seurat/seurat_5/environment.yml | 1 -
 seurat/seurat_5/install.R       | 3 +++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/seurat/seurat_5/environment.yml b/seurat/seurat_5/environment.yml
index a724b70b..38de64b1 100644
--- a/seurat/seurat_5/environment.yml
+++ b/seurat/seurat_5/environment.yml
@@ -5,7 +5,6 @@ channels:
 dependencies:
   - bioconductor-annotationdbi
   - bioconductor-biocparallel
-  - bioconductor-celldex>=1.16.0
   - bioconductor-genomeinfodbdata
   - bioconductor-glmgampoi
   - bioconductor-org.hs.eg.db
diff --git a/seurat/seurat_5/install.R b/seurat/seurat_5/install.R
index 153c8e72..7cb2a612 100644
--- a/seurat/seurat_5/install.R
+++ b/seurat/seurat_5/install.R
@@ -1,6 +1,9 @@
 #!/usr/bin/env Rscript
 args <- commandArgs(trailingOnly = TRUE)
 setRepositories(ind = 1:3)
+
+remotes::install_bioc("celldex", upgrade = "never")
+
 remotes::install_github("satijalab/seurat-wrappers@73466e3", upgrade = "never")
 
 # https://github.com/chris-mcginnis-ucsf/DoubletFinder/issues/244

From f0486d6ecca40cd8e5e4baca95d1193b98b7a0eb Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Wed, 19 Nov 2025 22:49:00 +0000
Subject: [PATCH 37/65] =?UTF-8?q?docs:=20=F0=9F=A4=96=20update=20readme=20?=
 =?UTF-8?q?for=20seurat/seurat=5F5/Dockerfile.v1=20(#326)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: 41898282+github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 seurat/seurat_5/v1-dev.README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/seurat/seurat_5/v1-dev.README.md b/seurat/seurat_5/v1-dev.README.md
index 3a809251..5d79f1e3 100644
--- a/seurat/seurat_5/v1-dev.README.md
+++ b/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/b238a7797ca293c2e7bce225fb0a98d31ec2b121/seurat/seurat_5/Dockerfile.v1
+Dockerfile source: https://github.com/CCBR/Dockers2/blob/b578b35c2ff345f8eb773641d1cd7f6bf5a47282/seurat/seurat_5/Dockerfile.v1
 
 
-Built on: 2025-11-10_20:55:00 
+Built on: 2025-11-19_22:26:40 
 
 Build tag: v1-dev 
 

From 465206d72c6f0016d1d3c955cce47e6dcb08c611 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Fri, 21 Nov 2025 10:57:30 -0500
Subject: [PATCH 38/65] fix: install gypsum before celldex

---
 seurat/seurat_5/install.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/seurat/seurat_5/install.R b/seurat/seurat_5/install.R
index 7cb2a612..65417899 100644
--- a/seurat/seurat_5/install.R
+++ b/seurat/seurat_5/install.R
@@ -2,6 +2,7 @@
 args <- commandArgs(trailingOnly = TRUE)
 setRepositories(ind = 1:3)
 
+remotes::install_cran("gypsum", repos = "https://bioc.r-universe.dev/", upgrade = "never")
 remotes::install_bioc("celldex", upgrade = "never")
 
 remotes::install_github("satijalab/seurat-wrappers@73466e3", upgrade = "never")
@@ -11,7 +12,6 @@ remotes::install_github("chris-mcginnis-ucsf/DoubletFinder@3b420df", upgrade = "
 
 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")
-remotes::install_cran("gypsum", repos = "https://bioc.r-universe.dev/", upgrade = "never")
 
 abort_packages_not_installed <- function(...) {
   package_status <- lapply(c(...), rlang::is_installed)
@@ -25,4 +25,4 @@ abort_packages_not_installed <- function(...) {
   }
 }
 
-abort_packages_not_installed('SeuratWrappers', 'DoubletFinder', 'Routliers', 'BPCells', 'gypsum')
+abort_packages_not_installed('SeuratWrappers', 'DoubletFinder', 'Routliers', 'BPCells', 'gypsum', 'celldex')

From 2961f57be8963fa43378ab1646954d092ab354df Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Fri, 21 Nov 2025 11:26:55 -0500
Subject: [PATCH 39/65] fix: install alabaster.base

---
 seurat/seurat_5/install.R | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/seurat/seurat_5/install.R b/seurat/seurat_5/install.R
index 65417899..766ccacc 100644
--- a/seurat/seurat_5/install.R
+++ b/seurat/seurat_5/install.R
@@ -2,6 +2,7 @@
 args <- commandArgs(trailingOnly = TRUE)
 setRepositories(ind = 1:3)
 
+remotes::install_cran("alabaster.base", repos = "https://bioc.r-universe.dev/", upgrade = "never")
 remotes::install_cran("gypsum", repos = "https://bioc.r-universe.dev/", upgrade = "never")
 remotes::install_bioc("celldex", upgrade = "never")
 
@@ -14,8 +15,10 @@ remotes::install_version("Routliers", repos = "https://cran.rstudio.com/", versi
 remotes::install_cran("BPCells", repos = "https://bnprks.r-universe.dev", upgrade = "never")
 
 abort_packages_not_installed <- function(...) {
-  package_status <- lapply(c(...), rlang::is_installed)
-  packages_not_installed <- Filter(isFALSE, package_status) |> unlist()
+  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: \n  ",

From 34971bf87f6882870f46845f488506fbb7dcf691 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Fri, 21 Nov 2025 12:32:08 -0500
Subject: [PATCH 40/65] fix: try install r-base 4.5

---
 seurat/seurat_5/environment.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/seurat/seurat_5/environment.yml b/seurat/seurat_5/environment.yml
index 38de64b1..becd4f17 100644
--- a/seurat/seurat_5/environment.yml
+++ b/seurat/seurat_5/environment.yml
@@ -9,11 +9,11 @@ dependencies:
   - bioconductor-glmgampoi
   - bioconductor-org.hs.eg.db
   - bioconductor-org.mm.eg.db
-  - bioconductor-orthology.eg.db=3.17.0
-  - bioconductor-scrnaseq=2.14.0
-  - bioconductor-singlecellexperiment=1.22.0
-  - bioconductor-singler=2
-  - r-base=4
+  - bioconductor-orthology.eg.db
+  - bioconductor-scrnaseq
+  - bioconductor-singlecellexperiment
+  - bioconductor-singler
+  - r-base=4.5
   - r-cluster
   - r-cluster=2
   - r-cowplot

From ad1666be85b0aaf96475008d78227fb49bcbd50f Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Fri, 21 Nov 2025 13:42:17 -0500
Subject: [PATCH 41/65] fix: try installing alabaster via conda

---
 seurat/seurat_5/environment.yml | 3 ++-
 seurat/seurat_5/install.R       | 1 -
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/seurat/seurat_5/environment.yml b/seurat/seurat_5/environment.yml
index becd4f17..b6bdbe79 100644
--- a/seurat/seurat_5/environment.yml
+++ b/seurat/seurat_5/environment.yml
@@ -3,6 +3,7 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
+  - bioconductor-alabaster.base
   - bioconductor-annotationdbi
   - bioconductor-biocparallel
   - bioconductor-genomeinfodbdata
@@ -13,7 +14,7 @@ dependencies:
   - bioconductor-scrnaseq
   - bioconductor-singlecellexperiment
   - bioconductor-singler
-  - r-base=4.5
+  - r-base=4.3
   - r-cluster
   - r-cluster=2
   - r-cowplot
diff --git a/seurat/seurat_5/install.R b/seurat/seurat_5/install.R
index 766ccacc..f85d5c7e 100644
--- a/seurat/seurat_5/install.R
+++ b/seurat/seurat_5/install.R
@@ -2,7 +2,6 @@
 args <- commandArgs(trailingOnly = TRUE)
 setRepositories(ind = 1:3)
 
-remotes::install_cran("alabaster.base", repos = "https://bioc.r-universe.dev/", upgrade = "never")
 remotes::install_cran("gypsum", repos = "https://bioc.r-universe.dev/", upgrade = "never")
 remotes::install_bioc("celldex", upgrade = "never")
 

From 587033b1015505b752c02993e990ede902436127 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 7 Jan 2026 10:32:54 -0500
Subject: [PATCH 42/65] style: auto format

---
 seurat/seurat_5/install.R | 35 +++++++++++++++++++++++++++++------
 1 file changed, 29 insertions(+), 6 deletions(-)

diff --git a/seurat/seurat_5/install.R b/seurat/seurat_5/install.R
index f85d5c7e..82004f62 100644
--- a/seurat/seurat_5/install.R
+++ b/seurat/seurat_5/install.R
@@ -2,16 +2,32 @@
 args <- commandArgs(trailingOnly = TRUE)
 setRepositories(ind = 1:3)
 
-remotes::install_cran("gypsum", repos = "https://bioc.r-universe.dev/", upgrade = "never")
+remotes::install_cran(
+  "gypsum",
+  repos = "https://bioc.r-universe.dev/",
+  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@3b420df", upgrade = "never")
+remotes::install_github(
+  "chris-mcginnis-ucsf/DoubletFinder@3b420df",
+  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")
+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(...)
@@ -20,11 +36,18 @@ abort_packages_not_installed <- function(...) {
   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: \n  ",
+      "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', 'celldex')
+abort_packages_not_installed(
+  'SeuratWrappers',
+  'DoubletFinder',
+  'Routliers',
+  'BPCells',
+  'gypsum',
+  'celldex'
+)

From c1008efdd41c37d911b0d84cde6add44a5acf1f3 Mon Sep 17 00:00:00 2001
From: Nathan Wong <nathan.wong@nih.gov>
Date: Fri, 20 Feb 2026 16:29:28 -0500
Subject: [PATCH 43/65] test: alabaster.base installation

---
 seurat/seurat_5/install.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/seurat/seurat_5/install.R b/seurat/seurat_5/install.R
index 82004f62..6686fc1e 100644
--- a/seurat/seurat_5/install.R
+++ b/seurat/seurat_5/install.R
@@ -49,5 +49,6 @@ abort_packages_not_installed(
   'Routliers',
   'BPCells',
   'gypsum',
-  'celldex'
+  'celldex',
+  'alabaster.base'
 )

From 0726b31085aefe0df74e1b43bd4aeace644cafbb Mon Sep 17 00:00:00 2001
From: Nathan Wong <nathan.wong@nih.gov>
Date: Fri, 20 Feb 2026 16:54:14 -0500
Subject: [PATCH 44/65] test: alabaster.base installation: list pos

---
 seurat/seurat_5/install.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/seurat/seurat_5/install.R b/seurat/seurat_5/install.R
index 6686fc1e..cc725e62 100644
--- a/seurat/seurat_5/install.R
+++ b/seurat/seurat_5/install.R
@@ -49,6 +49,6 @@ abort_packages_not_installed(
   'Routliers',
   'BPCells',
   'gypsum',
-  'celldex',
-  'alabaster.base'
+  'alabaster.base',
+  'celldex'
 )

From dbee6d4769a30a1d1555f7f7eacf243ba3c6adbe Mon Sep 17 00:00:00 2001
From: Nathan Wong <nathan.wong@nih.gov>
Date: Mon, 23 Feb 2026 09:22:21 -0500
Subject: [PATCH 45/65] fix: force alabaster.base installation

---
 seurat/seurat_5/install.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/seurat/seurat_5/install.R b/seurat/seurat_5/install.R
index cc725e62..2962dcb0 100644
--- a/seurat/seurat_5/install.R
+++ b/seurat/seurat_5/install.R
@@ -7,6 +7,7 @@ remotes::install_cran(
   repos = "https://bioc.r-universe.dev/",
   upgrade = "never"
 )
+remotes::install_bioc("alabaster.base", upgrade = "never")
 remotes::install_bioc("celldex", upgrade = "never")
 
 remotes::install_github("satijalab/seurat-wrappers@73466e3", upgrade = "never")

From db165c065dc9dcbb5637b2246dc8c88931f1e9e4 Mon Sep 17 00:00:00 2001
From: Nathan Wong <nathan.wong@nih.gov>
Date: Mon, 23 Feb 2026 09:44:54 -0500
Subject: [PATCH 46/65] fix: install assorthead as upstream dependency of
 alabaster.base and celldex

---
 seurat/seurat_5/install.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/seurat/seurat_5/install.R b/seurat/seurat_5/install.R
index 2962dcb0..f70730f5 100644
--- a/seurat/seurat_5/install.R
+++ b/seurat/seurat_5/install.R
@@ -7,6 +7,7 @@ remotes::install_cran(
   repos = "https://bioc.r-universe.dev/",
   upgrade = "never"
 )
+remotes::install("assorthead", upgrade = "never")
 remotes::install_bioc("alabaster.base", upgrade = "never")
 remotes::install_bioc("celldex", upgrade = "never")
 

From 4f9a9bcbbed34d785092c3fdf345f90b83268327 Mon Sep 17 00:00:00 2001
From: Nathan Wong <nathan.wong@nih.gov>
Date: Mon, 23 Feb 2026 10:07:47 -0500
Subject: [PATCH 47/65] fix: install assorthead as upstream dependency of
 alabaster.base and celldex

---
 seurat/seurat_5/install.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/seurat/seurat_5/install.R b/seurat/seurat_5/install.R
index f70730f5..13b7e240 100644
--- a/seurat/seurat_5/install.R
+++ b/seurat/seurat_5/install.R
@@ -7,7 +7,7 @@ remotes::install_cran(
   repos = "https://bioc.r-universe.dev/",
   upgrade = "never"
 )
-remotes::install("assorthead", upgrade = "never")
+remotes::install_bioc("assorthead", upgrade = "never")
 remotes::install_bioc("alabaster.base", upgrade = "never")
 remotes::install_bioc("celldex", upgrade = "never")
 

From b31df6a91dcad00238539019f6fda7e80aad8a1f Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Mon, 23 Feb 2026 10:33:09 -0500
Subject: [PATCH 48/65] fix: write R package versions as CSV

---
 seurat/seurat_5/Dockerfile.v1 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/seurat/seurat_5/Dockerfile.v1 b/seurat/seurat_5/Dockerfile.v1
index 48da0311..aa336bd4 100644
--- a/seurat/seurat_5/Dockerfile.v1
+++ b/seurat/seurat_5/Dockerfile.v1
@@ -22,7 +22,7 @@ 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 && \
-    R -s -e "readr::write_tsv(tibble::as_tibble(installed.packages()), '/data2/r-packages.tsv')"
+    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}

From 88a749b4184468c59c0e856d8d8dd17ce32d5ec7 Mon Sep 17 00:00:00 2001
From: Nathan Wong <nathan.wong@nih.gov>
Date: Mon, 23 Feb 2026 11:37:46 -0500
Subject: [PATCH 49/65] fix: update rdfh5 as upstream dependency of
 alabaster.base and celldex

---
 seurat/seurat_5/install.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/seurat/seurat_5/install.R b/seurat/seurat_5/install.R
index 13b7e240..ae89e911 100644
--- a/seurat/seurat_5/install.R
+++ b/seurat/seurat_5/install.R
@@ -7,6 +7,7 @@ remotes::install_cran(
   repos = "https://bioc.r-universe.dev/",
   upgrade = "never"
 )
+remotes::install_bioc("rdfh5", upgrade = "never")
 remotes::install_bioc("assorthead", upgrade = "never")
 remotes::install_bioc("alabaster.base", upgrade = "never")
 remotes::install_bioc("celldex", upgrade = "never")

From d628755a7c8ae025677c238530285fc3e95c52d7 Mon Sep 17 00:00:00 2001
From: Nathan Wong <nathan.wong@nih.gov>
Date: Mon, 23 Feb 2026 16:38:38 -0500
Subject: [PATCH 50/65] fix: update rdfh5 as upstream dependency of
 alabaster.base and celldex

---
 seurat/seurat_5/install.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/seurat/seurat_5/install.R b/seurat/seurat_5/install.R
index ae89e911..0abeeede 100644
--- a/seurat/seurat_5/install.R
+++ b/seurat/seurat_5/install.R
@@ -7,7 +7,7 @@ remotes::install_cran(
   repos = "https://bioc.r-universe.dev/",
   upgrade = "never"
 )
-remotes::install_bioc("rdfh5", upgrade = "never")
+remotes::install_bioc("rdfh5", upgrade = "never") 
 remotes::install_bioc("assorthead", upgrade = "never")
 remotes::install_bioc("alabaster.base", upgrade = "never")
 remotes::install_bioc("celldex", upgrade = "never")

From ae60fe51b0227c798b43c3ce0a134772ef76446d Mon Sep 17 00:00:00 2001
From: Nathan Wong <nathan.wong@nih.gov>
Date: Tue, 24 Feb 2026 09:18:01 -0500
Subject: [PATCH 51/65] fix: Update to Rv4.5 and add dependencies and direct
 load of celldex

---
 seurat/seurat_5/environment.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/seurat/seurat_5/environment.yml b/seurat/seurat_5/environment.yml
index b6bdbe79..939a3aca 100644
--- a/seurat/seurat_5/environment.yml
+++ b/seurat/seurat_5/environment.yml
@@ -14,7 +14,10 @@ dependencies:
   - bioconductor-scrnaseq
   - bioconductor-singlecellexperiment
   - bioconductor-singler
-  - r-base=4.3
+  - bioconductor-celldex
+  - bioconductor-rdfh5
+  - bioconductor-assorthead
+  - r-base=4.5
   - r-cluster
   - r-cluster=2
   - r-cowplot

From 2506aa6fca15d60b227183c6d253e9fd4dfe1982 Mon Sep 17 00:00:00 2001
From: Nathan Wong <nathan.wong@nih.gov>
Date: Tue, 24 Feb 2026 10:10:48 -0500
Subject: [PATCH 52/65] fix: Update rliger for Rv4.5

---
 seurat/seurat_5/environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/seurat/seurat_5/environment.yml b/seurat/seurat_5/environment.yml
index 939a3aca..4c899730 100644
--- a/seurat/seurat_5/environment.yml
+++ b/seurat/seurat_5/environment.yml
@@ -35,7 +35,7 @@ dependencies:
   - r-harmony>=0.1
   - r-hdf5r
   - r-httr2
-  - r-liger=1
+  - r-rliger=2.0
   - r-lubridate
   - r-png
   - r-presto

From cedcca63760a7b8a5b2f8b0a322fc57939a1f57b Mon Sep 17 00:00:00 2001
From: Nathan Wong <nathan.wong@nih.gov>
Date: Tue, 24 Feb 2026 11:46:36 -0500
Subject: [PATCH 53/65] fix: Update signac for Rv4.5

---
 seurat/seurat_5/environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/seurat/seurat_5/environment.yml b/seurat/seurat_5/environment.yml
index 4c899730..3791b0d4 100644
--- a/seurat/seurat_5/environment.yml
+++ b/seurat/seurat_5/environment.yml
@@ -46,7 +46,7 @@ dependencies:
   - r-r.utils
   - r-scales
   - r-seurat=5.3
-  - r-signac=1
+  - r-signac=1.16
   - r-stringr
   - r-tibble
   - r-tidyr

From 03818ef85758d097bc354977f6ef539b976eb94b Mon Sep 17 00:00:00 2001
From: Nathan Wong <nathan.wong@nih.gov>
Date: Tue, 24 Feb 2026 13:34:52 -0500
Subject: [PATCH 54/65] fix: Update signac for Rv4.5

---
 seurat/seurat_5/environment.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/seurat/seurat_5/environment.yml b/seurat/seurat_5/environment.yml
index 3791b0d4..21d201da 100644
--- a/seurat/seurat_5/environment.yml
+++ b/seurat/seurat_5/environment.yml
@@ -15,7 +15,7 @@ dependencies:
   - bioconductor-singlecellexperiment
   - bioconductor-singler
   - bioconductor-celldex
-  - bioconductor-rdfh5
+  - bioconductor-rhdf5
   - bioconductor-assorthead
   - r-base=4.5
   - r-cluster
@@ -35,7 +35,7 @@ dependencies:
   - r-harmony>=0.1
   - r-hdf5r
   - r-httr2
-  - r-rliger=2.0
+  - r-rliger=2.2.1
   - r-lubridate
   - r-png
   - r-presto
@@ -46,7 +46,7 @@ dependencies:
   - r-r.utils
   - r-scales
   - r-seurat=5.3
-  - r-signac=1.16
+  - r-Signac=1.16.0
   - r-stringr
   - r-tibble
   - r-tidyr

From 6be108e86574e7795427278c226850beb742ddf8 Mon Sep 17 00:00:00 2001
From: Nathan Wong <nathan.wong@nih.gov>
Date: Tue, 24 Feb 2026 13:54:41 -0500
Subject: [PATCH 55/65] fix: Update signac and rliger without version spec for
 Rv4.5

---
 seurat/seurat_5/environment.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/seurat/seurat_5/environment.yml b/seurat/seurat_5/environment.yml
index 21d201da..c946a0e3 100644
--- a/seurat/seurat_5/environment.yml
+++ b/seurat/seurat_5/environment.yml
@@ -35,7 +35,7 @@ dependencies:
   - r-harmony>=0.1
   - r-hdf5r
   - r-httr2
-  - r-rliger=2.2.1
+  - r-rliger
   - r-lubridate
   - r-png
   - r-presto
@@ -46,7 +46,7 @@ dependencies:
   - r-r.utils
   - r-scales
   - r-seurat=5.3
-  - r-Signac=1.16.0
+  - r-signac
   - r-stringr
   - r-tibble
   - r-tidyr

From a32840c2c260cc9e45a47a669ec66d8c8c2a003a Mon Sep 17 00:00:00 2001
From: Nathan Wong <nathan.wong@nih.gov>
Date: Tue, 24 Feb 2026 14:24:13 -0500
Subject: [PATCH 56/65] test: container without rliger and signac for Rv4.5

---
 seurat/seurat_5/environment.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/seurat/seurat_5/environment.yml b/seurat/seurat_5/environment.yml
index c946a0e3..0739b572 100644
--- a/seurat/seurat_5/environment.yml
+++ b/seurat/seurat_5/environment.yml
@@ -35,7 +35,7 @@ dependencies:
   - r-harmony>=0.1
   - r-hdf5r
   - r-httr2
-  - r-rliger
+ # - r-rliger
   - r-lubridate
   - r-png
   - r-presto
@@ -46,7 +46,7 @@ dependencies:
   - r-r.utils
   - r-scales
   - r-seurat=5.3
-  - r-signac
+#  - r-signac
   - r-stringr
   - r-tibble
   - r-tidyr

From 407d9845ae334b3f0708b9c4fe6cd9508ef76dd8 Mon Sep 17 00:00:00 2001
From: Nathan Wong <nathan.wong@nih.gov>
Date: Tue, 24 Feb 2026 14:57:17 -0500
Subject: [PATCH 57/65] test: downgrade from Rv4.5 to Rv4.4.3 for compatibility
 with other packages

---
 seurat/seurat_5/environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/seurat/seurat_5/environment.yml b/seurat/seurat_5/environment.yml
index 0739b572..15f63f59 100644
--- a/seurat/seurat_5/environment.yml
+++ b/seurat/seurat_5/environment.yml
@@ -17,7 +17,7 @@ dependencies:
   - bioconductor-celldex
   - bioconductor-rhdf5
   - bioconductor-assorthead
-  - r-base=4.5
+  - r-base=4.4.3
   - r-cluster
   - r-cluster=2
   - r-cowplot

From 71011f20368a5dff3765de3c823d21d3661df352 Mon Sep 17 00:00:00 2001
From: Nathan Wong <nathan.wong@nih.gov>
Date: Tue, 24 Feb 2026 15:47:24 -0500
Subject: [PATCH 58/65] test: Rv4.4.3 with primary installations in
 environment.yml

---
 seurat/seurat_5/install.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/seurat/seurat_5/install.R b/seurat/seurat_5/install.R
index 0abeeede..45ad58da 100644
--- a/seurat/seurat_5/install.R
+++ b/seurat/seurat_5/install.R
@@ -7,10 +7,10 @@ remotes::install_cran(
   repos = "https://bioc.r-universe.dev/",
   upgrade = "never"
 )
-remotes::install_bioc("rdfh5", upgrade = "never") 
-remotes::install_bioc("assorthead", upgrade = "never")
-remotes::install_bioc("alabaster.base", upgrade = "never")
-remotes::install_bioc("celldex", 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")
 

From 64ceb186e8cda6df95cfa74377a8ae306a5765c3 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Tue, 24 Feb 2026 21:09:18 +0000
Subject: [PATCH 59/65] =?UTF-8?q?docs:=20=F0=9F=A4=96=20update=20readme=20?=
 =?UTF-8?q?for=20seurat/seurat=5F5/Dockerfile.v1=20(#337)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: 41898282+github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 seurat/seurat_5/v1-dev.README.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/seurat/seurat_5/v1-dev.README.md b/seurat/seurat_5/v1-dev.README.md
index 5d79f1e3..6eabe396 100644
--- a/seurat/seurat_5/v1-dev.README.md
+++ b/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/b578b35c2ff345f8eb773641d1cd7f6bf5a47282/seurat/seurat_5/Dockerfile.v1
+Dockerfile source: https://github.com/CCBR/Dockers2/blob/dbbaf1e15b2914ffe7159183559ca5c0912b6876/seurat/seurat_5/Dockerfile.v1
 
 
-Built on: 2025-11-19_22:26:40 
+Built on: 2026-02-24_20:48:27 
 
 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 | 2025-10-21 |
+| 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 | 3.13.9 |
+| python3 | 3.14.3 |
 | qualimap | NOTINDOCKER |
 | rsem | NOTINDOCKER |
 | rseqc | NOTINDOCKER |

From 50dbd2cbd0a5cbcae895b00fabd86bf8504a29d7 Mon Sep 17 00:00:00 2001
From: Nathan Wong <nathan.wong@nih.gov>
Date: Tue, 24 Feb 2026 16:21:50 -0500
Subject: [PATCH 60/65] test: Rv4.4.3 with rliger and signac in environment.yml

---
 seurat/seurat_5/environment.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/seurat/seurat_5/environment.yml b/seurat/seurat_5/environment.yml
index 15f63f59..4a952546 100644
--- a/seurat/seurat_5/environment.yml
+++ b/seurat/seurat_5/environment.yml
@@ -35,7 +35,7 @@ dependencies:
   - r-harmony>=0.1
   - r-hdf5r
   - r-httr2
- # - r-rliger
+  - r-rliger
   - r-lubridate
   - r-png
   - r-presto
@@ -46,7 +46,7 @@ dependencies:
   - r-r.utils
   - r-scales
   - r-seurat=5.3
-#  - r-signac
+  - r-signac
   - r-stringr
   - r-tibble
   - r-tidyr

From 3a9334679d791f9a8a42c61e6abd4367599a487d Mon Sep 17 00:00:00 2001
From: Nathan Wong <nathan.wong@nih.gov>
Date: Tue, 24 Feb 2026 16:36:04 -0500
Subject: [PATCH 61/65] fix: r-liger name correction

---
 seurat/seurat_5/environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/seurat/seurat_5/environment.yml b/seurat/seurat_5/environment.yml
index 4a952546..634d4f7a 100644
--- a/seurat/seurat_5/environment.yml
+++ b/seurat/seurat_5/environment.yml
@@ -35,7 +35,7 @@ dependencies:
   - r-harmony>=0.1
   - r-hdf5r
   - r-httr2
-  - r-rliger
+  - r-r-liger
   - r-lubridate
   - r-png
   - r-presto

From 73ed8a7cb3057941301cc7bc991322c5955a3be9 Mon Sep 17 00:00:00 2001
From: Nathan Wong <nathan.wong@nih.gov>
Date: Wed, 25 Feb 2026 10:00:44 -0500
Subject: [PATCH 62/65] fix: install rliger via install.R

---
 seurat/seurat_5/environment.yml | 2 +-
 seurat/seurat_5/install.R       | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/seurat/seurat_5/environment.yml b/seurat/seurat_5/environment.yml
index 634d4f7a..5543b891 100644
--- a/seurat/seurat_5/environment.yml
+++ b/seurat/seurat_5/environment.yml
@@ -35,7 +35,7 @@ dependencies:
   - r-harmony>=0.1
   - r-hdf5r
   - r-httr2
-  - r-r-liger
+ # - r-r-liger
   - r-lubridate
   - r-png
   - r-presto
diff --git a/seurat/seurat_5/install.R b/seurat/seurat_5/install.R
index 45ad58da..8a895786 100644
--- a/seurat/seurat_5/install.R
+++ b/seurat/seurat_5/install.R
@@ -7,6 +7,7 @@ remotes::install_cran(
   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")

From c45eaabe1271f5093fecdec4c89037fe9744ab86 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Wed, 25 Feb 2026 15:25:37 +0000
Subject: [PATCH 63/65] =?UTF-8?q?docs:=20=F0=9F=A4=96=20update=20readme=20?=
 =?UTF-8?q?for=20seurat/seurat=5F5/Dockerfile.v1=20(#338)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: 41898282+github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 seurat/seurat_5/v1-dev.README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/seurat/seurat_5/v1-dev.README.md b/seurat/seurat_5/v1-dev.README.md
index 6eabe396..b846e69b 100644
--- a/seurat/seurat_5/v1-dev.README.md
+++ b/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/dbbaf1e15b2914ffe7159183559ca5c0912b6876/seurat/seurat_5/Dockerfile.v1
+Dockerfile source: https://github.com/CCBR/Dockers2/blob/7c5c4f081bda2bf7b62f95c0fe914ffbf60d0a15/seurat/seurat_5/Dockerfile.v1
 
 
-Built on: 2026-02-24_20:48:27 
+Built on: 2026-02-25_15:01:56 
 
 Build tag: v1-dev 
 

From 22414ed32acc09ea91d9067030706df28c138abb Mon Sep 17 00:00:00 2001
From: Nathan Wong <nathan.wong@nih.gov>
Date: Fri, 6 Mar 2026 15:31:51 -0500
Subject: [PATCH 64/65] fix: Update DoubletFinder version in install.R

---
 seurat/seurat_5/install.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/seurat/seurat_5/install.R b/seurat/seurat_5/install.R
index 8a895786..59856f06 100644
--- a/seurat/seurat_5/install.R
+++ b/seurat/seurat_5/install.R
@@ -17,7 +17,7 @@ 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@3b420df",
+  "chris-mcginnis-ucsf/DoubletFinder@aee4431",
   upgrade = "never"
 )
 

From a6b2c5bbe1de7e894334c7be060682559bc52e65 Mon Sep 17 00:00:00 2001
From: Nathan Wong <nathan.wong@nih.gov>
Date: Fri, 6 Mar 2026 15:32:17 -0500
Subject: [PATCH 65/65] fix: Update DoubletFinder version in install.R

---
 seurat/seurat_5/install.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/seurat/seurat_5/install.R b/seurat/seurat_5/install.R
index 59856f06..39399b46 100644
--- a/seurat/seurat_5/install.R
+++ b/seurat/seurat_5/install.R
@@ -19,7 +19,7 @@ remotes::install_github("satijalab/seurat-wrappers@73466e3", upgrade = "never")
 remotes::install_github(
   "chris-mcginnis-ucsf/DoubletFinder@aee4431",
   upgrade = "never"
-)
+) 
 
 remotes::install_version(
   "Routliers",