Merge branch 'main' into shinycell2_local_fixes

Author: rroutsong

config/cluster.json

@@ -17,9 +17,9 @@
         "time": "2-00:00:00"
     },
     "seuratQC": {
-	"threads": "8",
-	"mem": "150g",
-	"time": "1-00:00:00"
+        "threads": "8",
+        "mem": "150g",
+        "time": "1-00:00:00"
     },
     "aggregate": {
         "threads": "16",
@@ -29,7 +29,28 @@
     "seuratIntegrate": {
         "threads": "8",
         "mem": "350g",
-	"partition": "largemem",
+        "partition": "largemem",
         "time": "1-00:00:00"
+    },
+    "shinycodes": {
+        "threads": "16",
+        "mem": "32g",
+        "partition": "norm",
+        "time": "0-08:00:00",
+        "gres": "lscratch:100"
+    },
+    "shinyfiles": {
+        "threads": "16",
+        "mem": "32g",
+        "partition": "norm",
+        "time": "0-08:00:00",
+        "gres": "lscratch:100"
+    },
+    "shinytar": {
+        "threads": "32",
+        "mem": "64g",
+        "partition": "norm",
+        "time": "0-08:00:00",
+        "gres": "lscratch:100"
     }
-}
+}

docker/ShinyCell2/Dockerfile

@@ -0,0 +1,56 @@
+FROM rocker/shiny:4.4.3
+LABEL maintainer="Skyler Kuhn <kuhnsa@nih.gov>, Ryan Routsong <routsongrm@nih.gov>"
+RUN mkdir -p /opt2/work && mkdir -p /data2 
+WORKDIR /opt2
+ENV TZ=America/New_York
+RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime \
+        && echo $TZ > /etc/timezone
+ENV DEBIAN_FRONTEND=noninteractive
+RUN apt-get update \
+    && apt-get upgrade -y \
+    && apt-get install -y \
+        build-essential \
+        bzip2 \
+        ca-certificates \
+        cmake \
+        curl \
+        gawk \
+        git \
+        gzip \
+        libfreetype6-dev \
+        libgit2-dev \
+        libpng-dev \
+        libtiff5-dev \
+        libjpeg-dev \
+        libharfbuzz-dev \
+        libfribidi-dev \
+        libhdf5-dev \
+        libxml2-dev \
+        locales \
+        make \
+        python3 \
+        python3-pip \
+        unzip \
+        wget \
+        zlib1g-dev \
+        pigz \
+        vim \
+    && apt-get clean && apt-get purge \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+RUN localedef -i en_US -f UTF-8 en_US.UTF-8
+RUN ln -sf /usr/bin/python3 /usr/bin/python
+RUN mkdir -p /opt2/ \
+        && wget --no-check-certificate -O /opt2/which.tar.gz https://ftp.gnu.org/gnu/which/which-2.21.tar.gz \
+        && tar -xvf /opt2/which.tar.gz -C /opt2/ \
+        && rm /opt2/which.tar.gz \
+        && cd /opt2/which-2.21/ \
+        && ./configure --prefix=/opt2/which-2.21 \
+        && make \
+        && make install
+COPY install_packages.R /opt2/install_packages.R
+RUN cd /opt2 && Rscript /opt2/install_packages.R 
+COPY git_installs.sh /opt2/work/git_installs.sh
+RUN cd /opt2/work; ./git_installs.sh
+RUN Rscript -e 'remotes::install_github("OpenOmics/ShinyCell2@deg_page")'
+ADD build_shinycell.R /usr/bin/build_shinycell.R
+RUN chmod +x /usr/bin/build_shinycell.R