Automate Docker push

.github/workflows/r_package.yaml

@@ -34,3 +34,20 @@ jobs:
       - name: Check
         run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
         shell: Rscript {0}
+
+      - name: Get R package version
+        run: |
+          version=$(grep Version DESCRIPTION | grep -o "[0-9.]\+")
+          echo "packageVersion=${version}" >> $GITHUB_ENV
+        shell: bash {0}
+
+      - name: Build and push
+        uses: docker/build-push-action@v1
+        with:
+          push: true
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_TOKEN }}
+          repository: almurphy/scfdev
+          tag_with_ref: true
+          tag_with_sha: true
+          tags: ${{ github.repository }}:${{ env.packageVersion }}

Dockerfile

@@ -0,0 +1,179 @@
+#LABEL maintainer="Combiz Khozoie, Ph.D. c.khozoie@imperial.ac.uk, Alan Murphy, a.murphy@imperial.ac.uk"
+
+## Use rstudio installs binaries from RStudio's RSPM service by default, 
+## Uses the latest stable ubuntu, R and Bioconductor versions. Created on unbuntu 20.04, R 4.0 and BiocManager 3.12
+FROM rocker/rstudio
+
+
+## Add packages dependencies
+RUN apt-get update \
+	&& apt-get install -y --no-install-recommends apt-utils \
+	&& apt-get install -y --no-install-recommends \
+	## Basic deps
+	gdb \
+	libxml2-dev \
+	python3-pip \
+	libz-dev \
+	liblzma-dev \
+	libbz2-dev \
+	libpng-dev \
+	libgit2-dev \
+	## sys deps from bioc_full
+	pkg-config \
+	fortran77-compiler \
+	byacc \
+	automake \
+	curl \
+	## This section installs libraries
+	libpcre2-dev \
+	libnetcdf-dev \
+	libhdf5-serial-dev \
+	libfftw3-dev \
+	libopenbabel-dev \
+	libopenmpi-dev \
+	libxt-dev \
+	libudunits2-dev \
+	libgeos-dev \
+	libproj-dev \
+	libcairo2-dev \
+	libtiff5-dev \
+	libreadline-dev \
+	libgsl0-dev \
+	libgslcblas0 \
+	libgtk2.0-dev \
+	libgl1-mesa-dev \
+	libglu1-mesa-dev \
+	libgmp3-dev \
+	libhdf5-dev \
+	libncurses-dev \
+	libbz2-dev \
+	libxpm-dev \
+	liblapack-dev \
+	libv8-dev \
+	libgtkmm-2.4-dev \
+	libmpfr-dev \
+	libmodule-build-perl \
+	libapparmor-dev \
+	libprotoc-dev \
+	librdf0-dev \
+	libmagick++-dev \
+	libsasl2-dev \
+	libpoppler-cpp-dev \
+	libprotobuf-dev \
+	libpq-dev \
+	libperl-dev \
+	## software - perl extentions and modules
+	libarchive-extract-perl \
+	libfile-copy-recursive-perl \
+	libcgi-pm-perl \
+	libdbi-perl \
+	libdbd-mysql-perl \
+	libxml-simple-perl \
+	libmysqlclient-dev \
+	default-libmysqlclient-dev \
+	libgdal-dev \
+	## new libs
+	libglpk-dev \
+	## Databases and other software
+	sqlite \
+	openmpi-bin \
+	mpi-default-bin \
+	openmpi-common \
+	openmpi-doc \
+	tcl8.6-dev \
+	tk-dev \
+	default-jdk \
+	imagemagick \
+	tabix \
+	ggobi \
+	graphviz \
+	protobuf-compiler \
+	jags \
+	## Additional resources
+	xfonts-100dpi \
+	xfonts-75dpi \
+	biber \
+	libsbml5-dev \
+	&& apt-get clean \
+	&& rm -rf /var/lib/apt/lists/*
+
+RUN install2.r -e \
+testthat \
+covr \
+knitr \
+purrr \
+stringr \
+cli \
+dplyr \
+data.table \
+R.utils \
+vroom \
+ggpubr \
+ggplot2 \
+rmarkdown \
+rlang \
+future \
+future.apply \
+plotly \
+threejs \
+plyr \
+assertthat \
+httr \
+prettydoc \
+leaflet \
+gdtools \
+formattable \
+ggdendro \
+ggridges \
+cowplot \
+forcats \
+ggrepel \
+igraph \
+tibble \
+tidyr \
+tidyselect \
+tidyverse \
+ids \
+snow \
+remotes \
+rliger \
+argparse \
+Hmisc
+
+## Install remaining packages from source
+COPY ./misc/requirements-src.R .
+RUN Rscript requirements-src.R
+
+## Install Bioconductor packages
+COPY ./misc/requirements-bioc.R .
+RUN apt-get update \
+ && apt-get install -y --no-install-recommends \
+   libfftw3-dev \
+   gcc && apt-get clean \
+ && rm -rf /var/lib/apt/lists/*
+RUN Rscript -e 'requireNamespace("BiocManager"); BiocManager::install(ask=F);' \
+&& Rscript requirements-bioc.R
+
+## Install from GH the following
+RUN installGithub.r neurogenomics/EWCE \
+chris-mcginnis-ucsf/DoubletFinder \
+theislab/kBET \
+combiz/RANN.L1 \
+NathanSkene/One2One \
+hhoeflin/hdf5r \
+mojaveazure/loomR \
+cole-trapnell-lab/monocle3 \
+neurogenomics/scFlowExample \
+neurogenomics/scFlowData
+
+## Install scFlow package
+# Copy description
+WORKDIR scFlow
+ADD . .
+
+# Install R package from source
+RUN Rscript -e "remotes::install_local()"
+RUN rm -rf *
+
+## Check if scFlow installed
+#RUN R -e 'library(scFlow)'

R/model_celltype_freqs.R

@@ -27,7 +27,7 @@ model_celltype_freqs <- function(sce,
                                  var_order = NULL,
                                  ...) {
 
-  if (is.null(var_order)) { var_order <- levels(sce[[dependent_var]]) }
+  if (is.null(var_order)){ var_order <- levels(as.factor(sce[[dependent_var]]))}
   fargs <- c(as.list(environment()), list(...))
 
   cli::cli_h1("Modelling Cell-type Frequencies")

misc/requirements-bioc.R

@@ -0,0 +1,27 @@
+bioc_pkgs<-c(
+'biomaRt',
+'SingleCellExperiment',
+'SummarizedExperiment',
+'MAST',
+'limma',
+'scater',
+'ROntoTools',
+'BiocGenerics',
+'S4Vectors',
+'IRanges',
+'GenomicRanges',
+'DelayedArray',
+'graphite',
+'batchelor',
+'DelayedMatrixStats',
+#'monocle3',#won't install correctly, known issue for docker 
+'DropletUtils',
+'multtest',
+'graph',
+'rhdf5',
+'preprocessCore',
+'BiocStyle'
+)
+
+requireNamespace("BiocManager")
+BiocManager::install(bioc_pkgs,ask=F)

misc/requirements-src.R

@@ -0,0 +1,32 @@
+#base r packages used - no need to install
+#utils, Matrix, stats, methods
+
+pkgs <- c(
+'spelling',
+'english',
+'Seurat',
+'DT',
+'sctransform',
+'RcppParallel',
+'bib2df',
+'paletteer',
+'WebGestaltR',
+'uniftest',
+'Matrix.utils',
+#'rliger',
+'qs',
+'UpSetR',
+'nVennR',
+'DirichletReg',
+'enrichR',
+'Rtsne',
+'BiocManager',
+'Rcpp',
+'RcppArmadillo',
+'RcppEigen',
+'RcppProgress'
+
+)
+
+
+install.packages(pkgs)