Merge branch 'GalaxyCLI' of https://github.com/NIDAP-Community/SCWorkflow into GalaxyCLI

Author: phoman14

.github/environment.yml

@@ -0,0 +1,72 @@
+name: scworkflow
+channels:
+  - conda-forge
+  - bioconda
+  - seqera
+dependencies:
+  - r-base=4.1.3
+  - bioconductor-celldex
+  - r-colorspace
+  - bioconductor-complexheatmap = 2.10.0
+  - r-cowplot = 1.1.1
+  - r-data.table = 1.14.8
+  - r-dendextend
+  - r-dendsort
+  - r-digest = 0.6.31
+  - r-dplyr = 1.1.1
+  - bioconductor-edgeR = 3.36.0
+  - r-future >= 1.27.0
+  - r-future.apply >= 1.9.0
+  - r-gargle >= 1.2.0
+  - r-gdata
+  - r-ggExtra
+  - r-ggplot2 >= 3.3.6
+  - r-ggplot2 < 4.0.0
+  - r-ggpubr >= 0.4.0
+  - r-ggrepel
+  - r-globals >= 0.16.1
+  - r-glue
+  - r-gridBase >= 0.4-7
+  - r-gridExtra >= 2.3
+  - r-gtable >= 0.3.1
+  - r-harmony >= 0.1.1
+  - r-hdf5r >= 1.3.5
+  - r-htmlwidgets
+  - r-httpuv >= 1.6.5
+  - r-httr
+  - r-jsonlite
+  - r-leiden >= 0.4.2
+  - bioconductor-limma >= 3.50.3
+  - r-magrittr >= 2.0.3
+  - r-markdown >= 1.1
+  - bioconductor-MAST = 1.20.0
+  - r-Matrix = 1.5.4.1
+  - r-pheatmap
+  - r-plotly >= 4.10.0
+  - r-plyr
+  - r-png
+  - r-progressr >= 0.10.1
+  - r-pryr >= 0.1.5
+  - r-purrr >= 0.3.4
+  - r-quantmod >= 0.4.20
+  - r-RColorBrewer >= 1.1-3
+  - r-reshape2 >= 1.4.4
+  - r-reticulate >= 1.25
+  - r-rlang >= 1.0.6
+  - r-scales
+  - bioconductor-scDblFinder = 1.8.0
+  - r-Seurat = 4.1.1
+  - r-SeuratObject = 4.1.3
+  - bioconductor-singler = 1.8.0
+  - r-statmod >= 1.4.37
+  - r-stringr
+  - r-svglite >= 2.1.0
+  - r-tibble >= 3.1.8
+  - r-tidyr
+  - r-tidyverse >= 1.3.2
+  - r-viridisLite >= 0.4.0
+  - r-xfun >= 0.32
+  - r-zip >= 2.2.0
+  - r-knitr
+  - r-markdown
+  - r-testthat >= 3.0.0

Dockerfile

@@ -1,4 +1,4 @@
-FROM rocker/tidyverse:4.3.2
+FROM nciccbr/ccbr_ubuntu_base_20.04:v7
 
 # build time variables
 ARG BUILD_DATE="000000"
@@ -13,113 +13,15 @@ SHELL ["/bin/bash", "-lc"]
 RUN chmod 777 /usr/local/lib/R/site-library /usr/local/lib/R/library
 
 # 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
+COPY .github/environment.yml /data2/
+ENV CONDA_ENV=scw
+RUN conda update -n base -c conda-forge conda && \
+    mamba env create -n ${CONDA_ENV} -f /data2/environment.yml && \
+    echo "conda activate ${CONDA_ENV}" > ~/.bashrc && \
+    chmod -R a+rx /opt2
+ENV PATH="/opt2/conda/envs/${CONDA_ENV}/bin:$PATH"
+ENV R_LIBS_USER="/opt2/conda/envs/${CONDA_ENV}/lib/R/library/"
+COPY .github/install.R /data2/
 
 # install R package
 COPY . /opt2/SCWorkflow