✨ new scrna qc docker (#249)

* 🎉 create image to perform hbc scrna qc

* :oencil: added missing optparse package

* 🔨 Added packages for h5 compatibility

* 🔧 added missing package

* 🔧 fix COPY ref

* update docker table (#250)

Co-authored-by: migbro <migbro@users.noreply.github.com>

* Update hbc_scrna_qc/v1.0.0-scrnaseq/Dockerfile

Co-authored-by: Dan Miller <dmiller15@users.noreply.github.com>

* 📝 rename to fix exact release name from source material

* update docker table (#251)

Co-authored-by: migbro <migbro@users.noreply.github.com>

---------

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: migbro <migbro@users.noreply.github.com>
Co-authored-by: Dan Miller <dmiller15@users.noreply.github.com>

README.md

@@ -82,6 +82,7 @@ gatk|4.beta.6|docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk:4.beta.6
 gatk|4.beta.6-tabix|docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk:4.beta.6-tabix
 gatk|latest|docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk:latest
 gistic|latest|docker pull pgc-images.sbgenomics.com/d3b-bixu/gistic:latest
+hbc_scrna_qc|scrnaseq|docker pull pgc-images.sbgenomics.com/d3b-bixu/hbc_scrna_qc:scrnaseq
 hisat2|2.2.1|docker pull pgc-images.sbgenomics.com/d3b-bixu/hisat2:2.2.1
 hotspots|0.1.0|docker pull pgc-images.sbgenomics.com/d3b-bixu/hotspots:0.1.0
 intervar|v2.2.1|docker pull pgc-images.sbgenomics.com/d3b-bixu/intervar:v2.2.1

hbc_scrna_qc/scrnaseq/Dockerfile

@@ -0,0 +1,16 @@
+FROM rocker/tidyverse:4.4.0
+LABEL maintainer="Miguel Brown (brownm28@chop.edu)"
+LABEL description="Docker image to run Harvard Bioinformatics Core (HBC) scRNA QC as defined here: https://github.com/hbctraining/scRNA-seq_online?tab=readme-ov-file#installation-requirements. Install specific version of Seurat for downstream compatibility"
+
+ENV DEBIAN_FRONTEND=noninteractive
+# Install dependencies so that a specific version of Seurat can be installed
+ENV SEURAT_VERSION=4.3.0.1
+ENV SEURATOBJECT_VERSION=4.1.3
+ENV SEURAT_URL=https://cran.r-project.org/src/contrib/Archive/Seurat/Seurat_${SEURAT_VERSION}.tar.gz
+ENV SEURATOBJECT_URL=https://cran.r-project.org/src/contrib/Archive/SeuratObject/SeuratObject_${SEURATOBJECT_VERSION}.tar.gz
+
+RUN apt update -y && apt install -y libbz2-dev libglpk40 libhdf5-dev patch
+RUN  mkdir ~/.R && echo MAKEFLAGS = -j8 > ~/.R/Makevars && R -e "BiocManager::install(c('AnnotationHub', 'ensembldb', 'multtest', 'glmGamPoi'))"
+RUN R -e "install.packages(c('optparse', 'cowplot', 'fitdistrplus', 'future', 'future.apply', 'ggrepel', 'ggridges', 'ica', 'igraph', 'irlba', 'leiden', 'lmtest', 'matrixStats', 'patchwork', 'pbapply', 'plotly', 'png', 'progressr', 'RANN', 'RcppAnnoy', 'reticulate', 'ROCR', 'Rtsne', 'scattermore', 'sctransform', 'spatstat.explore', 'spatstat.geom', 'uwot', 'RcppEigen', 'RcppProgress', 'sp', 'metap', 'hdf5r', 'patch'), type='source', Ncpus=8)"
+RUN R -e "install.packages(c('${SEURATOBJECT_URL}','${SEURAT_URL}'), repos=NULL, type='source', Ncpus=8)"
+COPY Dockerfile .