diff --git a/Dockerfile b/Dockerfile index 7c4d029..c7f8aa8 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,14 +1,16 @@ -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 ${DOWNLOAD_URL} \ @@ -16,17 +18,7 @@ RUN curl -o cellranger-${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-${VDJ_REFERENCE_VERSION} /opt/ +# Removing VDJ reference data compared to previous version to make the container smaller WORKDIR /opt diff --git a/Dockerfile.cromwell b/Dockerfile.cromwell index 4644a72..15bdb5c 100644 --- a/Dockerfile.cromwell +++ b/Dockerfile.cromwell @@ -1,14 +1,16 @@ -FROM centos:7 +FROM almalinux/amd64:9.3-base-20231124 -LABEL maintainer="Jaeyoung Chun (chunj@mskcc.org)" +# CentOS 8 is dead, so we are using AlmaLinux 8.9. Built by Oracle. + +LABEL maintainer="Tobias Krause (krauset@mskcc.org)" ARG CELLRANGER_VERSION -ARG VDJ_REFERENCE_VERSION ARG DOWNLOAD_URL ENV PATH /opt/cellranger-${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 ${DOWNLOAD_URL} \ @@ -16,17 +18,7 @@ RUN curl -o cellranger-${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..ddd427a 100755 --- a/build.sh +++ b/build.sh @@ -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=${version} . # hack: comment the ENTRYPOINT and CMD lines to make it work for cromwell @@ -36,8 +36,8 @@ cat Dockerfile \ # build cromwell-${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=${version} \ -f Dockerfile.cromwell . diff --git a/config.sh b/config.sh index d14df04..8eab7db 100644 --- a/config.sh +++ b/config.sh @@ -1,8 +1,8 @@ -version="7.0.0" -vdj_ref_version="7.0.0" +version="8.0.0" site_url="https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/7.0/" -download_url="" +download_url="https://cf.10xgenomics.com/releases/cell-exp/cellranger-8.0.0.tar.gz?Expires=1714715076&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=iMQiaG3m8-8s3nkOq2v~lxbxErGe9SdbG4XF-lpoFmaSg3gPjneGlNWorqY6AvMx3jsHznRwXz3N3ZI5f39Xd0RofGh8j9N0RW0eiNMwoSq53isUyjYQlcxIOfbh9FTHNXO8aRc0oa7I5Uyz-W6hVRekGCYPk~ErtkNOCIjbHhHgj9kF5pazLAyquKUuOHJ6uEL72ISAGYtVgcOEgnXOIirwdRHxraeuFuCnPJS9Bp05XOhFS1hGB8Sd7TxYHMaJ1-MVV1BdGUJCIGb8Sx~iGV32DLI13UI~ZV64kLjUr2bYzWsSULyPwbGhv-x5TaHM24DB5mGO1D36B1QhSYTXfw__" # docker related -registry="quay.io/hisplan" -image_name="cellranger" +registry="docker.io" +image_cellranger_name="sailmskcc/cellranger" +image_cromwell_name="sailmskcc/cromwell-cellranger" diff --git a/push.sh b/push.sh index 1a86db5..b433346 100755 --- a/push.sh +++ b/push.sh @@ -2,7 +2,7 @@ source config.sh -echo "${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} +docker push ${registry}/${image_cellranger_name}:${version} +docker push ${registry}/${image_cromwell_name}:${version} diff --git a/run-smoke-test.sh b/run-smoke-test.sh index 71c6cf0..7ef8d16 100755 --- a/run-smoke-test.sh +++ b/run-smoke-test.sh @@ -4,16 +4,16 @@ source config.sh # cellranger docker run -it --rm \ - cellranger:${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