From 8a6300c0da39b3f46522561b95da9b7de206466e Mon Sep 17 00:00:00 2001
From: Andrew Moorman <andrewmoormanmskcc@gmail.com>
Date: Tue, 4 Apr 2023 17:07:32 -0400
Subject: [PATCH 1/6] Updated to CellRanger 7.1.0

---
 Dockerfile          | 4 ++--
 Dockerfile.cromwell | 4 ++--
 config.sh           | 6 +++---
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 7c4d029..eaae42b 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -16,13 +16,13 @@ RUN curl -o cellranger-${CELLRANGER_VERSION}.tar.gz ${DOWNLOAD_URL} \
     && rm -rf cellranger-${CELLRANGER_VERSION}.tar.gz \
     && mv cellranger-${CELLRANGER_VERSION} /opt/
 
-# V(D)J GRCh38 Reference - 7.0.0 (May 17, 2022)
+# V(D)J GRCh38 Reference - 7.1.0 (Dec 7, 2022)
 RUN curl -O https://cf.10xgenomics.com/supp/cell-vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
     && tar xzf refdata-cellranger-vdj-GRCh38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
     && rm -rf refdata-cellranger-vdj-GRCh38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
     && mv refdata-cellranger-vdj-GRCh38-alts-ensembl-${VDJ_REFERENCE_VERSION} /opt/
 
-# V(D)J GRCm38 Reference - 7.0.0 (May 17, 2022)
+# V(D)J GRCm38 Reference - 7.1.0 (Dec 7, 2022)
 RUN curl -O https://cf.10xgenomics.com/supp/cell-vdj/refdata-cellranger-vdj-GRCm38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
     && tar xzf refdata-cellranger-vdj-GRCm38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
     && rm -rf refdata-cellranger-vdj-GRCm38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
diff --git a/Dockerfile.cromwell b/Dockerfile.cromwell
index 4644a72..58aca38 100644
--- a/Dockerfile.cromwell
+++ b/Dockerfile.cromwell
@@ -16,13 +16,13 @@ RUN curl -o cellranger-${CELLRANGER_VERSION}.tar.gz ${DOWNLOAD_URL} \
     && rm -rf cellranger-${CELLRANGER_VERSION}.tar.gz \
     && mv cellranger-${CELLRANGER_VERSION} /opt/
 
-# V(D)J GRCh38 Reference - 7.0.0 (May 17, 2022)
+# V(D)J GRCh38 Reference - 7.1.0 (Dec 7, 2022)
 RUN curl -O https://cf.10xgenomics.com/supp/cell-vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
     && tar xzf refdata-cellranger-vdj-GRCh38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
     && rm -rf refdata-cellranger-vdj-GRCh38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
     && mv refdata-cellranger-vdj-GRCh38-alts-ensembl-${VDJ_REFERENCE_VERSION} /opt/
 
-# V(D)J GRCm38 Reference - 7.0.0 (May 17, 2022)
+# V(D)J GRCm38 Reference - 7.1.0 (Dec 7, 2022)
 RUN curl -O https://cf.10xgenomics.com/supp/cell-vdj/refdata-cellranger-vdj-GRCm38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
     && tar xzf refdata-cellranger-vdj-GRCm38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
     && rm -rf refdata-cellranger-vdj-GRCm38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
diff --git a/config.sh b/config.sh
index d14df04..4b4b7e7 100644
--- a/config.sh
+++ b/config.sh
@@ -1,6 +1,6 @@
-version="7.0.0"
-vdj_ref_version="7.0.0"
-site_url="https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/7.0/"
+version="7.1.0"
+vdj_ref_version="7.1.0"
+site_url="https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/7.1/"
 download_url=""
 
 # docker related

From c538673459bd2870e0be6949d23d17dafc693a6e Mon Sep 17 00:00:00 2001
From: Andrew Moorman <andrewmoormanmskcc@gmail.com>
Date: Tue, 4 Apr 2023 17:28:24 -0400
Subject: [PATCH 2/6] Reverted CR VDJ version to 7.0.0; CR's v7.1.0 tar.gz file
 is corrupted

---
 config.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config.sh b/config.sh
index 4b4b7e7..191185a 100644
--- a/config.sh
+++ b/config.sh
@@ -1,5 +1,5 @@
 version="7.1.0"
-vdj_ref_version="7.1.0"
+vdj_ref_version="7.0.0"
 site_url="https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/7.1/"
 download_url=""
 

From 2e93bcc2af096374fa33763ebd2e98725882384f Mon Sep 17 00:00:00 2001
From: Tobias Krause <tobiaspk1@gmail.com>
Date: Thu, 2 May 2024 21:42:56 -0400
Subject: [PATCH 3/6] Update to version 8.0.0. Move builds to SAIL from quay
 and hisplan

---
 Dockerfile          | 19 +++++--------------
 Dockerfile.cromwell | 19 +++++--------------
 LICENSE             |  2 +-
 README.md           |  9 +++------
 build.sh            |  6 ++----
 config.sh           | 10 +++++-----
 push.sh             |  6 +++---
 7 files changed, 24 insertions(+), 47 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 7c4d029..ad764af 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,9 +1,10 @@
-FROM centos:7
+FROM almalinux:8.9
 
-LABEL maintainer="Jaeyoung Chun (chunj@mskcc.org)"
+# CentOS 8 is dead, so we are using AlmaLinux 8.9. Built by Oracle.
+
+LABEL maintainer="Tobias Krause (krauset@mskcc.org)"
 
 ARG CELLRANGER_VERSION
-ARG VDJ_REFERENCE_VERSION
 ARG DOWNLOAD_URL
 ENV PATH /opt/cellranger-${CELLRANGER_VERSION}:$PATH
 
@@ -16,17 +17,7 @@ RUN curl -o cellranger-${CELLRANGER_VERSION}.tar.gz ${DOWNLOAD_URL} \
     && rm -rf cellranger-${CELLRANGER_VERSION}.tar.gz \
     && mv cellranger-${CELLRANGER_VERSION} /opt/
 
-# V(D)J GRCh38 Reference - 7.0.0 (May 17, 2022)
-RUN curl -O https://cf.10xgenomics.com/supp/cell-vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
-    && tar xzf refdata-cellranger-vdj-GRCh38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
-    && rm -rf refdata-cellranger-vdj-GRCh38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
-    && mv refdata-cellranger-vdj-GRCh38-alts-ensembl-${VDJ_REFERENCE_VERSION} /opt/
-
-# V(D)J GRCm38 Reference - 7.0.0 (May 17, 2022)
-RUN curl -O https://cf.10xgenomics.com/supp/cell-vdj/refdata-cellranger-vdj-GRCm38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
-    && tar xzf refdata-cellranger-vdj-GRCm38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
-    && rm -rf refdata-cellranger-vdj-GRCm38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
-    && mv refdata-cellranger-vdj-GRCm38-alts-ensembl-${VDJ_REFERENCE_VERSION} /opt/
+# Removing VDJ reference data compared to previous version to make the container smaller
 
 WORKDIR /opt
 
diff --git a/Dockerfile.cromwell b/Dockerfile.cromwell
index 4644a72..fb34eae 100644
--- a/Dockerfile.cromwell
+++ b/Dockerfile.cromwell
@@ -1,9 +1,10 @@
-FROM centos:7
+FROM almalinux:8.9
 
-LABEL maintainer="Jaeyoung Chun (chunj@mskcc.org)"
+# CentOS 8 is dead, so we are using AlmaLinux 8.9. Built by Oracle.
+
+LABEL maintainer="Tobias Krause (krauset@mskcc.org)"
 
 ARG CELLRANGER_VERSION
-ARG VDJ_REFERENCE_VERSION
 ARG DOWNLOAD_URL
 ENV PATH /opt/cellranger-${CELLRANGER_VERSION}:$PATH
 
@@ -16,17 +17,7 @@ RUN curl -o cellranger-${CELLRANGER_VERSION}.tar.gz ${DOWNLOAD_URL} \
     && rm -rf cellranger-${CELLRANGER_VERSION}.tar.gz \
     && mv cellranger-${CELLRANGER_VERSION} /opt/
 
-# V(D)J GRCh38 Reference - 7.0.0 (May 17, 2022)
-RUN curl -O https://cf.10xgenomics.com/supp/cell-vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
-    && tar xzf refdata-cellranger-vdj-GRCh38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
-    && rm -rf refdata-cellranger-vdj-GRCh38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
-    && mv refdata-cellranger-vdj-GRCh38-alts-ensembl-${VDJ_REFERENCE_VERSION} /opt/
-
-# V(D)J GRCm38 Reference - 7.0.0 (May 17, 2022)
-RUN curl -O https://cf.10xgenomics.com/supp/cell-vdj/refdata-cellranger-vdj-GRCm38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
-    && tar xzf refdata-cellranger-vdj-GRCm38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
-    && rm -rf refdata-cellranger-vdj-GRCm38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
-    && mv refdata-cellranger-vdj-GRCm38-alts-ensembl-${VDJ_REFERENCE_VERSION} /opt/
+# Removing VDJ reference data compared to previous version to make the container smaller
 
 WORKDIR /opt
 
diff --git a/LICENSE b/LICENSE
index 59f69b0..9556eba 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2019 - 2022 Jaeyoung Chun
+Copyright (c) 2019 - 2022 Jaeyoung Chun, Tobias Krause
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
diff --git a/README.md b/README.md
index a66a394..3af92ce 100644
--- a/README.md
+++ b/README.md
@@ -1,14 +1,11 @@
 # docker-cellranger
 
-Dockerized Cell Ranger v7.0.0
+Dockerized Cell Ranger v8.0.0
 
 - GEX: https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/7.0/
 - VDJ: https://support.10xgenomics.com/single-cell-vdj/software/downloads/7.0/
 
-Reference dataset included:
-
-- Human reference dataset (GRCh38/Ensembl/10x) required for Cell Ranger V(D)J
-- Mouse reference dataset (GRCm38/Ensembl/10x) required for Cell Ranger V(D)J
+Version 7.2 supports Flex + CITE, Version 8.0 supports Visium HD.
 
 ## License
 
@@ -38,7 +35,7 @@ conda activate scing
 
 ```bash
 $ cellranger --help
-cellranger cellranger-7.0.0
+cellranger cellranger-8.0.0
 Process 10x Genomics Gene Expression, Feature Barcode, and Immune Profiling data
 
 USAGE:
diff --git a/build.sh b/build.sh
index 0e7a925..6d028b8 100755
--- a/build.sh
+++ b/build.sh
@@ -22,9 +22,8 @@ fi
 
 # build ${image_name}:${version}
 docker build \
-    --tag ${image_name}:${version} \
+    --tag ${image_cellranger_name}:${version} \
     --build-arg DOWNLOAD_URL=${download_url} \
-    --build-arg VDJ_REFERENCE_VERSION=${vdj_ref_version} \
     --build-arg CELLRANGER_VERSION=${version} .
 
 # hack: comment the ENTRYPOINT and CMD lines to make it work for cromwell
@@ -36,8 +35,7 @@ cat Dockerfile \
 
 # build cromwell-${image_name}:${version}
 docker build \
-    --tag cromwell-${image_name}:${version} \
+    --tag cromwell-${image_cromwell_name}:${version} \
     --build-arg DOWNLOAD_URL=${download_url} \
-    --build-arg VDJ_REFERENCE_VERSION=${vdj_ref_version} \
     --build-arg CELLRANGER_VERSION=${version} \
     -f Dockerfile.cromwell .
diff --git a/config.sh b/config.sh
index d14df04..8eab7db 100644
--- a/config.sh
+++ b/config.sh
@@ -1,8 +1,8 @@
-version="7.0.0"
-vdj_ref_version="7.0.0"
+version="8.0.0"
 site_url="https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/7.0/"
-download_url=""
+download_url="https://cf.10xgenomics.com/releases/cell-exp/cellranger-8.0.0.tar.gz?Expires=1714715076&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=iMQiaG3m8-8s3nkOq2v~lxbxErGe9SdbG4XF-lpoFmaSg3gPjneGlNWorqY6AvMx3jsHznRwXz3N3ZI5f39Xd0RofGh8j9N0RW0eiNMwoSq53isUyjYQlcxIOfbh9FTHNXO8aRc0oa7I5Uyz-W6hVRekGCYPk~ErtkNOCIjbHhHgj9kF5pazLAyquKUuOHJ6uEL72ISAGYtVgcOEgnXOIirwdRHxraeuFuCnPJS9Bp05XOhFS1hGB8Sd7TxYHMaJ1-MVV1BdGUJCIGb8Sx~iGV32DLI13UI~ZV64kLjUr2bYzWsSULyPwbGhv-x5TaHM24DB5mGO1D36B1QhSYTXfw__"
 
 # docker related
-registry="quay.io/hisplan"
-image_name="cellranger"
+registry="docker.io"
+image_cellranger_name="sailmskcc/cellranger"
+image_cromwell_name="sailmskcc/cromwell-cellranger"
diff --git a/push.sh b/push.sh
index 1a86db5..1bb5169 100755
--- a/push.sh
+++ b/push.sh
@@ -2,7 +2,7 @@
 
 source config.sh
 
-echo "${registry}/${image_name}:${version}"
+echo "${registry}/${image_cellranger_name}:${version}"
 
-scing push --image=${registry}/${image_name}:${version}
-scing push --image=${registry}/cromwell-${image_name}:${version}
+scing push --image=${registry}/${image_cellranger_name}:${version}
+scing push --image=${registry}/cromwell-${image_cromwell_name}:${version}

From ea191c57ef26a4f3ded0fe4d254be904c37dfb90 Mon Sep 17 00:00:00 2001
From: Tobias Krause <tobiaspk1@gmail.com>
Date: Thu, 2 May 2024 21:56:41 -0400
Subject: [PATCH 4/6] Use amd64 built

---
 Dockerfile          | 5 +++--
 Dockerfile.cromwell | 5 +++--
 build.sh            | 2 ++
 3 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index ad764af..67ad5ef 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM almalinux:8.9
+FROM almalinux/amd64:8.5
 
 # CentOS 8 is dead, so we are using AlmaLinux 8.9. Built by Oracle.
 
@@ -9,7 +9,8 @@ ARG DOWNLOAD_URL
 ENV PATH /opt/cellranger-${CELLRANGER_VERSION}:$PATH
 
 RUN yum group install -y "Development Tools" \
-    && yum install -y which
+    && yum install -y which \
+    && yum install -y glibc
 
 # cell ranger binaries
 RUN curl -o cellranger-${CELLRANGER_VERSION}.tar.gz ${DOWNLOAD_URL} \
diff --git a/Dockerfile.cromwell b/Dockerfile.cromwell
index fb34eae..000e499 100644
--- a/Dockerfile.cromwell
+++ b/Dockerfile.cromwell
@@ -1,4 +1,4 @@
-FROM almalinux:8.9
+FROM almalinux/amd64:8.9
 
 # CentOS 8 is dead, so we are using AlmaLinux 8.9. Built by Oracle.
 
@@ -9,7 +9,8 @@ ARG DOWNLOAD_URL
 ENV PATH /opt/cellranger-${CELLRANGER_VERSION}:$PATH
 
 RUN yum group install -y "Development Tools" \
-    && yum install -y which
+    && yum install -y which \
+    && yum install -y glibc
 
 # cell ranger binaries
 RUN curl -o cellranger-${CELLRANGER_VERSION}.tar.gz ${DOWNLOAD_URL} \
diff --git a/build.sh b/build.sh
index 6d028b8..b08d05d 100755
--- a/build.sh
+++ b/build.sh
@@ -23,6 +23,7 @@ fi
 # build ${image_name}:${version}
 docker build \
     --tag ${image_cellranger_name}:${version} \
+    --platform linux/amd64 \
     --build-arg DOWNLOAD_URL=${download_url} \
     --build-arg CELLRANGER_VERSION=${version} .
 
@@ -36,6 +37,7 @@ cat Dockerfile \
 # build cromwell-${image_name}:${version}
 docker build \
     --tag cromwell-${image_cromwell_name}:${version} \
+    --platform linux/amd64 \
     --build-arg DOWNLOAD_URL=${download_url} \
     --build-arg CELLRANGER_VERSION=${version} \
     -f Dockerfile.cromwell .

From eab57adcededcb56ed1743f55c2df94c4ea295f7 Mon Sep 17 00:00:00 2001
From: Tobias Krause <tobiaspk1@gmail.com>
Date: Thu, 2 May 2024 22:14:10 -0400
Subject: [PATCH 5/6] Fix almalinux version for amd64 support

---
 Dockerfile          | 6 +++---
 Dockerfile.cromwell | 6 +++---
 run-smoke-test.sh   | 8 ++++----
 3 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 67ad5ef..c7f8aa8 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM almalinux/amd64:8.5
+FROM almalinux/amd64:9.3-base-20231124
 
 # CentOS 8 is dead, so we are using AlmaLinux 8.9. Built by Oracle.
 
@@ -9,8 +9,8 @@ ARG DOWNLOAD_URL
 ENV PATH /opt/cellranger-${CELLRANGER_VERSION}:$PATH
 
 RUN yum group install -y "Development Tools" \
-    && yum install -y which \
-    && yum install -y glibc
+    && yum install -y which 
+    #&& yum install -y glibc
 
 # cell ranger binaries
 RUN curl -o cellranger-${CELLRANGER_VERSION}.tar.gz ${DOWNLOAD_URL} \
diff --git a/Dockerfile.cromwell b/Dockerfile.cromwell
index 000e499..15bdb5c 100644
--- a/Dockerfile.cromwell
+++ b/Dockerfile.cromwell
@@ -1,4 +1,4 @@
-FROM almalinux/amd64:8.9
+FROM almalinux/amd64:9.3-base-20231124
 
 # CentOS 8 is dead, so we are using AlmaLinux 8.9. Built by Oracle.
 
@@ -9,8 +9,8 @@ ARG DOWNLOAD_URL
 ENV PATH /opt/cellranger-${CELLRANGER_VERSION}:$PATH
 
 RUN yum group install -y "Development Tools" \
-    && yum install -y which \
-    && yum install -y glibc
+    && yum install -y which 
+    #&& yum install -y glibc
 
 # cell ranger binaries
 RUN curl -o cellranger-${CELLRANGER_VERSION}.tar.gz ${DOWNLOAD_URL} \
diff --git a/run-smoke-test.sh b/run-smoke-test.sh
index 71c6cf0..7ef8d16 100755
--- a/run-smoke-test.sh
+++ b/run-smoke-test.sh
@@ -4,16 +4,16 @@ source config.sh
 
 # cellranger
 docker run -it --rm \
-    cellranger:${version} --help
+    ${image_cellranger_name}:${version} --help
 
 # cellranger count
 docker run -it --rm \
-    cellranger:${version} count --help
+    ${image_cellranger_name}:${version} count --help
 
 # cellranger vdj
 docker run -it --rm \
-    cellranger:${version} vdj --help
+    ${image_cellranger_name}:${version} vdj --help
 
 # cellranger version
 docker run -it --rm \
-    cellranger:${version} --version
+    ${image_cellranger_name}:${version} --version

From cce587587e66e6ff105f3d22946f8745595fe965 Mon Sep 17 00:00:00 2001
From: Tobias Krause <tobiaspk1@gmail.com>
Date: Thu, 2 May 2024 22:23:34 -0400
Subject: [PATCH 6/6] Fix docker image names, remove SCING dependency for push

---
 build.sh | 2 +-
 push.sh  | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/build.sh b/build.sh
index b08d05d..ddd427a 100755
--- a/build.sh
+++ b/build.sh
@@ -36,7 +36,7 @@ cat Dockerfile \
 
 # build cromwell-${image_name}:${version}
 docker build \
-    --tag cromwell-${image_cromwell_name}:${version} \
+    --tag ${image_cromwell_name}:${version} \
     --platform linux/amd64 \
     --build-arg DOWNLOAD_URL=${download_url} \
     --build-arg CELLRANGER_VERSION=${version} \
diff --git a/push.sh b/push.sh
index 1bb5169..b433346 100755
--- a/push.sh
+++ b/push.sh
@@ -4,5 +4,5 @@ source config.sh
 
 echo "${registry}/${image_cellranger_name}:${version}"
 
-scing push --image=${registry}/${image_cellranger_name}:${version}
-scing push --image=${registry}/cromwell-${image_cromwell_name}:${version}
+docker push ${registry}/${image_cellranger_name}:${version}
+docker push ${registry}/${image_cromwell_name}:${version}