-
-
Save Blanketjack/5b2dd99f3d8f4d0976303db591429e7f to your computer and use it in GitHub Desktop.
Single cell environment 0.6.0 dockerfile
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
FROM bioconductor/bioconductor_docker:RELEASE_3_12 | |
RUN Rscript -e "\ | |
BiocManager::install(c(\ | |
'AnnotationDbi', \ | |
'AnnotationFilter', \ | |
'BiocGenerics', \ | |
'EnsDb.Mmusculus.v79', \ | |
'EnsDb.Hsapiens.v75', \ | |
'GenomeInfoDb', \ | |
'GenomicFeatures', \ | |
'GenomicRanges', \ | |
'ggbio', \ | |
'IRanges', \ | |
'MAST', \ | |
'motifmatchr', \ | |
'multtest', \ | |
'Rsamtools', \ | |
'S4Vectors', \ | |
'ggbio', \ | |
'motifmatchr')); \ | |
install.packages(c(\ | |
'cowplot', \ | |
'dplyr', \ | |
'ggplot2',\ | |
'hdf5r',\ | |
'patchwork',\ | |
'reticulate', \ | |
'Seurat', \ | |
'Signac', \ | |
'tidyverse'));" | |
RUN Rscript -e "\ | |
BiocManager::install(c( \ | |
'DelayedArray', \ | |
'DelayedMatrixStats', \ | |
'limma', \ | |
'SingleCellExperiment', \ | |
'SummarizedExperiment', \ | |
'batchelor', \ | |
'Matrix.utils')); \ | |
library(devtools);" | |
RUN Rscript -e "install.packages('metap')" | |
RUN wget -P /tmp https://repo.anaconda.com/miniconda/Miniconda3-py37_4.8.2-Linux-x86_64.sh && \ | |
sha256sum /tmp/Miniconda3-py37_4.8.2-Linux-x86_64.sh && \ | |
bash /tmp/Miniconda3-py37_4.8.2-Linux-x86_64.sh -p /miniconda -b && \ | |
rm /tmp/Miniconda3-py37_4.8.2-Linux-x86_64.sh | |
ENV PATH=/miniconda/bin:${PATH} | |
RUN mkdir -p /root/.local/share && \ | |
echo "/miniconda/bin/conda" > /root/.local/share/r-miniconda | |
RUN Rscript -e "\ | |
library(reticulate); \ | |
conda_install(env_name='umap-learn', packages='umap-learn');" | |
RUN apt-get update && \ | |
apt-get install -y libxkbcommon-x11-0 && \ | |
wget -P /tmp/ https://download1.rstudio.org/desktop/bionic/amd64/rstudio-1.2.5033-amd64.deb && \ | |
dpkg -i /tmp/rstudio-1.2.5033-amd64.deb | |
RUN apt-get install -y libboost-all-dev && \ | |
Rscript -e "\ | |
BiocManager::install('pcaMethods'); \ | |
library(devtools);" |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
cleared