changes from git pull

Author: phoman14

.github/workflows/docker.yml

@@ -2,13 +2,20 @@ name: docker
 
 on:
   workflow_dispatch:
+    inputs:
+      version_tag:
+        type: string
+        description: Container version tag. If not set, it will be created automatically based on the released version and commit hash.
+        required: false
+        default: ''
   release:
     types: [published]
 
 env:
   IMAGE_NAME: "scworkflow" # must be lowercase
   CONTEXT: "./"
   NAMESPACE: "nciccbr"
+  USE_INPUT_TAG: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.version_tag != '' }}
 
 permissions: read-all
 
@@ -23,9 +30,15 @@ jobs:
           echo "DATE=$(date +"%Y-%m-%d")" >> "$GITHUB_OUTPUT"
 
           if [ '${{ github.event_name }}' == 'release' ]; then
+            # include latest tag since this is a release
             VERSION=${{ github.ref_name }}
             DOCKER_TAGS=${{ env.NAMESPACE }}/${{ env.IMAGE_NAME }}:${VERSION},${{ env.NAMESPACE }}/${{ env.IMAGE_NAME }}:latest
+          elif [ '${{ env.USE_INPUT_TAG }}' == 'true' ]; then
+            # use manual tag
+            VERSION=${{ github.event.inputs.version_tag }}
+            DOCKER_TAGS=${{ env.NAMESPACE }}/${{ env.IMAGE_NAME }}:${VERSION}
           else
+            # set tag from last release and current commit
             HASH=$(git rev-parse --short HEAD)
             VERSION="$(grep 'Version:' $CONTEXT/DESCRIPTION | sed 's/Version: /v/')_${HASH}"
             DOCKER_TAGS=${{ env.NAMESPACE }}/${{ env.IMAGE_NAME }}:${VERSION}
@@ -35,9 +48,9 @@ jobs:
 
       - name: debug
         run: |
-          echo "the github tag is ${{ github.ref_name }}"
-          echo "github event_name is ${{ github.event_name }}"
-          echo "the version tag is ${{ steps.vars.outputs.VERSION_TAG }}"
+          echo "Github tag: ${{ github.ref_name }}"
+          echo "Github event_name: ${{ github.event_name }}"
+          echo "Container version tag: ${{ steps.vars.outputs.VERSION_TAG }}"
 
       - name: Login to DockerHub
         if: ${{ github.event_name != 'pull_request' }}
@@ -49,11 +62,10 @@ jobs:
         uses: docker/build-push-action@v4
         with:
           push: ${{ github.event_name != 'pull_request' }}
-          tags: ${{ steps.vars.outputs.DOCKER_TAGS }} # include 'latest' tag if this is a release
+          tags: ${{ steps.vars.outputs.DOCKER_TAGS }}
           context: ${{ env.CONTEXT }}
           file: ${{ env.CONTEXT }}/Dockerfile
           build-args: |
             BUILD_DATE=${{ steps.vars.outputs.DATE }}
             BUILD_TAG=${{ steps.vars.outputs.VERSION_TAG }}
             REPONAME=${{ env.IMAGE_NAME }}
-            R_VERSION=4.3.2

DESCRIPTION

@@ -29,7 +29,6 @@ Depends:
     R (>= 4.0)
 Imports:
     anndata (>= 0.7.5.2),
-    BiocManager,
     callr (>= 3.7.1),
     celldex,
     colorspace,
@@ -65,6 +64,7 @@ Imports:
     magrittr (>= 2.0.3),
     markdown (>= 1.1),
     MAST (>= 1.20.0),
+    Matrix,
     methods (>= 4.1.3),
     pheatmap,
     plotly (>= 4.10.0),
@@ -80,9 +80,16 @@ Imports:
     rlang (>= 1.0.6),
     scales,
     scDblFinder,
+<<<<<<< HEAD
     Seurat (== 4.3.0),
     SeuratObject (== 4.1.3),
     Matrix (>= 1.6.1),
+=======
+    Seurat (< 5.0.0),
+    Seurat (>= 4.3.0),
+    SeuratObject (< 5.0.0),
+    SeuratObject (>= 4.1.3),
+>>>>>>> 6e803673e7a9d5a6e43342924bf3c18b8fee4fdf
     SingleR (>= 1.8.1),
     statmod (>= 1.4.37),
     stringr (>= 1.4.1),

Dockerfile

@@ -1,4 +1,4 @@
-FROM nciccbr/ccbr_ubuntu_22.04:v4
+FROM rocker/tidyverse:4.3.2
 
 # build time variables
 ARG BUILD_DATE="000000"
@@ -8,65 +8,130 @@ ENV BUILD_TAG=${BUILD_TAG}
 ARG REPONAME="000000"
 ENV REPONAME=${REPONAME}
 
-ARG R_VERSION=4.3.2
-ENV R_VERSION=${R_VERSION}
-
 SHELL ["/bin/bash", "-lc"]
 
-# Install conda and give write permissions to conda folder
-RUN echo 'export PATH=/opt2/conda/bin:$PATH' > /etc/profile.d/conda.sh && \
-    wget --quiet "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" -O ~/miniforge3.sh && \
-    /bin/bash ~/miniforge3.sh -b -p /opt2/conda && \
-    rm ~/miniforge3.sh && chmod 777 -R /opt2/conda/
-ENV PATH="/opt2/conda/bin:$PATH"
-
-# Pin channels and update
-RUN conda config --add channels conda-forge \
- && conda config --add channels bioconda \
- && conda config --set channel_priority strict
+RUN chmod 777 /usr/local/lib/R/site-library /usr/local/lib/R/library
 
-# install conda packages
-RUN mamba install -y -c conda-forge \
-    r-base=${R_VERSION} \
-    r-devtools r-testthat \
-    r-anndata \
-    r-callr r-colorspace r-cowplot \
-    r-data.table r-dendextend r-dendsort r-digest r-dplyr \
-    r-future r-future.apply \
-    r-gargle r-gdata r-ggExtra r-ggplot2 r-ggpubr r-ggrepel r-globals r-glue r-gridBase r-gridExtra r-gtable \
-    r-harmony r-hdf5r r-htmlwidgets r-httpuv r-httr \
-    r-jsonlite \
-    r-leiden \
-    r-magrittr r-markdown r-MAST r-methods \
-    r-pheatmap r-plotly r-plyr r-png r-progressr r-pryr r-purrr \
-    r-quantmod \
-    r-RColorBrewer r-reshape2 r-reticulate r-rlang \
-    r-scales r-Seurat r-statmod r-stringr r-svglite \
-    r-tibble r-tidyr r-tidyverse \
-    r-viridisLite \
-    r-xfun \
-    r-zip \
-    bioconductor-celldex bioconductor-ComplexHeatmap \
-    bioconductor-edger \
-    bioconductor-limma \
-    bioconductor-scDblFinder bioconductor-SingleR \
-    bioconductor-genomicranges \
-    bioconductor-summarizedexperiment \
-  && conda clean -afy
+# https://github.com/Bioconductor/bioconductor_docker/blob/7335f85420199679432d2a328c3a59b551b6cfd0/bioc_scripts/install_bioc_sysdeps.sh
+RUN apt-get update && apt-get upgrade -y && \
+  apt-get install -y --no-install-recommends --allow-unauthenticated \
+	automake \
+	biber \
+	byacc \
+	cmake \
+	coinor-libcgl-dev \
+	coinor-libsymphony-dev \
+	coinor-libsymphony-doc \
+	curl \
+	default-jdk \
+	default-libmysqlclient-dev \
+	fortran77-compiler \
+	ggobi \
+	graphviz \
+	imagemagick \
+	jags \
+	libapparmor-dev \
+	libarchive-dev \
+	libarchive-extract-perl \
+	libavfilter-dev \
+	libboost-dev \
+	libbz2-dev \
+	libcairo2-dev \
+	libcgi-pm-perl \
+	libdbd-mysql-perl \
+	libdbi-perl \
+	libeigen3-dev \
+	libfftw3-dev \
+	libfile-copy-recursive-perl \
+	libfuse-dev \
+	libgdal-dev \
+	libgeos-dev \
+	libgit2-dev \
+	libgl1-mesa-dev \
+	libglpk-dev \
+	libglu1-mesa-dev \
+	libgmp3-dev \
+	libgsl0-dev \
+	libgslcblas0 \
+	libgtk2.0-dev \
+	libgtkmm-2.4-dev \
+	libhdf5-dev \
+	libhdf5-serial-dev \
+	libhiredis-dev \
+	libjpeg-dev \
+	libjpeg-turbo8-dev \
+	libjpeg8-dev \
+	liblapack-dev \
+	liblzma-dev \
+	libmagick++-dev \
+	libmodule-build-perl \
+	libmpfr-dev \
+	libmysqlclient-dev \
+	libncurses-dev \
+	libnetcdf-dev \
+	libopenbabel-dev \
+	libopenmpi-dev \
+	libpcre2-dev \
+	libperl-dev \
+	libpng-dev \
+	libpoppler-cpp-dev \
+	libpoppler-glib-dev \
+	libpq-dev \
+	libproj-dev \
+	libprotobuf-dev \
+	libprotoc-dev \
+	librdf0-dev \
+	libreadline-dev \
+	librtmp-dev \
+	libsasl2-dev \
+	libsbml5-dev \
+	libssl-dev \
+	libtiff5-dev \
+	libudunits2-dev \
+	libv8-dev \
+	libxml-simple-perl \
+	libxml2-dev \
+	libxpm-dev \
+	libxt-dev \
+	libz-dev \
+	libzmq3-dev \
+	mono-runtime \
+	mpi-default-bin \
+	ocl-icd-opencl-dev \
+	openmpi-bin \
+	openmpi-common \
+	openmpi-doc \
+	protobuf-compiler \
+	python3-pip \
+	sqlite3 \
+	tabix \
+	tcl8.6-dev \
+	tk-dev \
+	xfonts-100dpi \
+	xfonts-75dpi \
+ 	liblz4-dev \
+    automake \
+    cmake \
+    default-jre \
+    g++ \
+    gcc \
+    gdb \
+    gfortran \
+    libcurl4-gnutls-dev \
+    make \
+    pkg-config
 
 # install R package
 COPY . /opt2/SCWorkflow
-RUN R -e "devtools::install_local('/opt2/SCWorkflow', dependencies = TRUE, repos='http://cran.rstudio.com')"
+RUN R -e 'remotes::install_version("Seurat", version="4.3.0"); remotes::install_version("SeuratObject", version="4.1.3")' && \
+  R -e "remotes::install_local('/opt2/SCWorkflow', dependencies = TRUE, upgrade='never', repos='http://cran.rstudio.com'); library(SCWorkflow)" && \
+  R -s -e "readr::write_tsv(tibble::as_tibble(installed.packages()), '/mnt/r-packages.tsv')"
 
 # add scworkflow exec to the path
-RUN chmod -R +x /opt2/conda/lib/R/library/SCWorkflow/exec
-ENV PATH="$PATH:/opt2/conda/lib/R/library/SCWorkflow/exec"
+RUN chmod -R +x /usr/local/lib/R/site-library/SCWorkflow/exec
+ENV PATH="$PATH:/usr/local/lib/R/site-library/SCWorkflow/exec"
 RUN scworkflow --help
 
-# copy example script & json to data
-COPY ./inst/extdata/TestRunjson.sh /data2/
-COPY ./inst/extdata/json_args/ /data2/json_args/
-
 # Save Dockerfile in the docker
 COPY Dockerfile /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
 RUN chmod a+r /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}

R/cli.R

@@ -124,7 +124,6 @@ Main functions:
   scworkflow heatmapSC
   scworkflow tSNE3D
   scworkflow dualLabeling
-
   scworkflow harmonyBatchCorrect
 "
   writeLines(usage, con = con)
@@ -200,35 +199,26 @@ cli_from_json <- function(method, json, debug = FALSE) {
         "object_input_rds must be included in the JSON because `object` is required for {method}()"
       )
     )
-    # most SCWorkflow functions return a list containing an "object" element plus a list of plots or other output.
-    # here we extract only the "object" element to pass as the first argument to this function.
-    object_list <- readr::read_rds(json_args[["object_input_rds"]])
-    print(paste0("Input List Names: ",paste(names(object_list), collapse = ", ")))
-
-    if (!(any(grepl("object|Object", names(object_list))))) {
-      message('Expected `object_input_rds` to contain an element with the name "object".')
-      object_list[["object"]] <- object_list
-    }
-    fcn_args[[first_arg]] <- object_list[["object"]]
+    fcn_args[[first_arg]] <- readr::read_rds(json_args[["object_input_rds"]])
   }
 
   ## If any arguments end in .txt, read them in as tables
   ## This is a bit hacky, but allows us to pass tables as arguments via json
   ## Adding logic to unlist parameters that should be vectors ( such as sample names)
-  
-  for(x in names(json_args)){
+  for(x in names(json_args)) {
     if(any(stringr::str_detect(json_args[[x]], glue::glue(".txt$")))){
-      json_args[[x]]=read.delim(json_args[[x]])
+      json_args[[x]] <- read.delim(json_args[[x]])
     }else if(any(stringr::str_detect(json_args[[x]], glue::glue(".csv$")))){  
-      json_args[[x]]=read.delim(json_args[[x]], sep=",")
+      json_args[[x]] <- read.delim(json_args[[x]], sep=",")
     }
-    if(class(json_args[[x]])=='list'){
+    if(class(json_args[[x]]) == 'list'){
       json_args[[x]] <- unlist(json_args[[x]])
     }
   }
 
-  # all other json keys should be arguments for the method
-  fcn_args <- c(fcn_args, json_args[!stringr::str_detect(names(json_args), "object_.*_rds")])
+  # remove object_input_rds, object_output_rds, and plot_output_rds.
+  # all other json keys should be arguments for the method.
+  fcn_args <- c(fcn_args, json_args[!stringr::str_detect(names(json_args), "object_.*_rds|plot_output_rds")])
 
   # invoke method with parsed arguments from json
   expr <- as.call(fcn_args)
@@ -240,7 +230,10 @@ cli_from_json <- function(method, json, debug = FALSE) {
 
     # save result to output_rds
     if ("object_output_rds" %in% names(json_args)) {
-      readr::write_rds(result, json_args[["object_output_rds"]])
+      readr::write_rds(result[['object']], json_args[["object_output_rds"]])
+    }
+    if ("plot_output_rds" %in% names(json_args)) {
+      readr::write_rds(result[['plot']], json_args[["plot_output_rds"]])
     }
   }
 

inst/extdata/json_args/colorByGene.json

@@ -1,6 +1,7 @@
 {
     "object_input_rds": "chariou/SCWorkflowObject_reclusterFilteredSeuratObject.rds",
     "object_output_rds": "chariou/SCWorkflowObject_colorByGene.rds",
+    "plot_output_rds": "chariou/plots/colorByGene.rds",
     "samples.to.include": ["CD8dep","NHSIL12"],
     "gene": "Cxcl3"
 }

inst/extdata/json_args/dotPlotMet.json

@@ -1,6 +1,7 @@
 {
     "object_input_rds": "chariou/SCWorkflowObject_reclusterFilteredSeuratObject.rds",
     "object_output_rds": "chariou/SCWorkflowObject_dotPlotMet.rds",
+    "plot_output_rds": "chariou/plots/dotPlotMet.rds",
     "metadata": "orig.ident",
     "cells": ["CD8dep","NHSIL12"],
     "markers": ["Il1b","Cxcr3"]

inst/extdata/json_args/heatmapSC.json

@@ -1,6 +1,7 @@
 {
     "object_input_rds": "chariou/SCWorkflowObject_reclusterFilteredSeuratObject.rds",
     "object_output_rds": "chariou/SCWorkflowObject_heatmapSC.rds",
+    "plot_output_rds": "chariou/plots/heatmapSC.rds",
     "sample.names": ["CD8dep","NHSIL12"],
     "metadata": ["orig.ident","immgen_main"],
     "transcripts": ["S100a8", "Il1b", "Cxcl3", "Lyz2", "Mmp12", "Cxcl10", "Ccl3", "Thy1", "Tmsb4x", "Cd8b1"]

inst/extdata/json_args/plotMetadata.json

@@ -1,6 +1,7 @@
 {
     "object_input_rds": "chariou/SCWorkflowObject_reclusterFilteredSeuratObject.rds",
     "object_output_rds": "chariou/SCWorkflowObject_plotMetadata.rds",
+    "plot_output_rds": "chariou/plots/plotMetadata.rds",
     "samples.to.include": ["CD8dep","NHSIL12"],
     "metadata.to.plot": ["orig.ident","pct_counts_in_top_20_genes"],
     "columns.to.summarize": null

inst/extdata/json_args/reclusterFilteredSeuratObject.json

@@ -1,5 +1,6 @@
 {
     "object_input_rds": "chariou/SCWorkflowObject_filterSeuratObjectByMetadata.rds",
     "object_output_rds": "chariou/SCWorkflowObject_reclusterFilteredSeuratObject.rds",
+    "plot_output_rds": "chariou/plots/reclusterFilteredSeuratObject_plots.rds",
     "old.columns.to.save": null
 }

inst/extdata/json_args/reclusterSeuratObject.json

@@ -1,5 +1,6 @@
 {
     "object_input_rds": "chariou/SCWorkflowObject_filterSeuratObjectByMetadata.rds",
     "object_output_rds": "chariou/SCWorkflowObject_reclusterSeuratObject.rds",
+    "plot_output_rds": "chariou/plots/reclusterSeuratObject.rds",
     "old.columns.to.save": null
 }