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Dev #2

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8a6300c
Updated to CellRanger 7.1.0
andrewmoorman Apr 4, 2023
c538673
Reverted CR VDJ version to 7.0.0; CR's v7.1.0 tar.gz file is corrupted
andrewmoorman Apr 4, 2023
2e93bcc
Update to version 8.0.0. Move builds to SAIL from quay and hisplan
Tobiaspk May 3, 2024
7da1f11
Merge remote-tracking branch 'upstream/master' into dev
Tobiaspk May 3, 2024
ea191c5
Use amd64 built
Tobiaspk May 3, 2024
eab57ad
Fix almalinux version for amd64 support
Tobiaspk May 3, 2024
cce5875
Fix docker image names, remove SCING dependency for push
Tobiaspk May 3, 2024
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22 changes: 7 additions & 15 deletions Dockerfile
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@@ -1,32 +1,24 @@
FROM centos:7
FROM almalinux/amd64:9.3-base-20231124

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

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 ${DOWNLOAD_URL} \
&& tar xzf cellranger-${CELLRANGER_VERSION}.tar.gz \
&& 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

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22 changes: 7 additions & 15 deletions Dockerfile.cromwell
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FROM centos:7
FROM almalinux/amd64:9.3-base-20231124

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

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 ${DOWNLOAD_URL} \
&& tar xzf cellranger-${CELLRANGER_VERSION}.tar.gz \
&& 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

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2 changes: 1 addition & 1 deletion LICENSE
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@@ -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
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9 changes: 3 additions & 6 deletions README.md
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# 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

Expand Down Expand Up @@ -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:
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8 changes: 4 additions & 4 deletions build.sh
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Expand Up @@ -22,9 +22,9 @@ fi

# build ${image_name}:${version}
docker build \
--tag ${image_name}:${version} \
--tag ${image_cellranger_name}:${version} \
--platform linux/amd64 \
--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
Expand All @@ -36,8 +36,8 @@ cat Dockerfile \

# build cromwell-${image_name}:${version}
docker build \
--tag cromwell-${image_name}:${version} \
--tag ${image_cromwell_name}:${version} \
--platform linux/amd64 \
--build-arg DOWNLOAD_URL=${download_url} \
--build-arg VDJ_REFERENCE_VERSION=${vdj_ref_version} \
--build-arg CELLRANGER_VERSION=${version} \
-f Dockerfile.cromwell .
10 changes: 5 additions & 5 deletions config.sh
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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"
6 changes: 3 additions & 3 deletions push.sh
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Expand Up @@ -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}
docker push ${registry}/${image_cellranger_name}:${version}
docker push ${registry}/${image_cromwell_name}:${version}
8 changes: 4 additions & 4 deletions run-smoke-test.sh
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Expand Up @@ -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