Init commit

.gitignore

+# Compiled Object files
+*.slo
+*.lo
+*.o
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+
+# build trees
+DEBUG*/*
+BUILD*/*
+RELEASE*/*
+TEST*/*
+
+# cmake
+CMakeCache.txt
+CMakeFiles
+Makefile
+cmake_install.cmake
+install_manifest.txt
+
+# vim 
+~*
+*.swp
+*.swo
+
+# python
+__pycache__/
+*.py[cod]
+*$py.class
+.ipynb_checkpoints

.gitlab-ci.yml

+image: eicweb.phy.anl.gov:4567/containers/image_recipes/root_base:latest
+#
+stages:
+  - phase1
+  - phase2
+
+eic_docker:
+  stage: phase1
+  tags:
+     - eic0 docker
+  script:
+     - cd containers/docker
+     - make login
+     - make release 
+
+eic_singularity:
+  stage: phase2
+  tags:
+     - singularity
+  script:
+     - cp containers/singularity/eic.def .
+     - /bin/bash .gitlabci/setup.sh
+     - /bin/bash .gitlabci/build.sh eic.def
+     - mkdir -p build 
+     - cp eic.sif build/.
+     - cp eic.def build/.
+
+  # This is where you can save job artifacts
+  # https://docs.gitlab.com/ee/user/project/pipelines/job_artifacts.html
+  # You can specify the path to containers or the build folder to save.
+  # Don't forget to save your recipes too!
+  artifacts:
+      paths:
+        - build/eic.sif
+        - build/eic.def
+
+

.gitlabci/build.sh

+#!/bin/bash
+
+# build.sh will build a Singularity container. It's not overly complicated.
+#
+# USAGE: build.sh --uri collection-name/container-name --cli registry Singularity
+#        build.sh --uri collection-name/container-name --cli registry
+#        build.sh Singularity
+
+# Copyright (C) 2017-2018 Vanessa Sochat.
+
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Affero General Public
+# License for more details.
+
+# You should have received a copy of the GNU Affero General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+set -o errexit
+set -o nounset
+
+function usage() {
+
+    echo "USAGE: build [recipe] [options]"
+    echo ""
+    echo "OPTIONS:
+
+          Image Format
+              --uri   -u    if uploading, a uri to give to sregistry
+              --cli   -c    the sregistry client to use (if uploading)
+              --help  -h    show this help and exit
+              "
+}
+
+# --- Option processing --------------------------------------------------------
+
+uri=""
+cli=""
+tag=""
+
+while true; do
+    case ${1:-} in
+        -h|--help|help)
+            usage
+            exit 0
+        ;;
+        -u|-uri)
+            shift
+            uri="${1:-}"
+            shift
+        ;;
+        -t|--tag)
+            shift
+            tag="${1:-}"
+            shift
+        ;;
+        -c|--cli)
+            shift
+            cli="${1:-}"
+            shift
+        ;;
+        \?) printf "illegal option: -%s\n" "${1:-}" >&2
+            usage
+            exit 1
+        ;;
+        -*)
+            printf "illegal option: -%s\n" "${1:-}" >&2
+            usage
+            exit 1
+        ;;
+        *)
+            break;
+        ;;
+    esac
+done
+
+################################################################################
+### Recipe File ################################################################
+################################################################################
+
+
+if [ $# == 0 ] ; then
+    recipe="Singularity"
+else
+    recipe=$1
+fi
+
+echo ""
+echo "Image Recipe: ${recipe}"
+
+
+################################################################################
+### Storage Client #############################################################
+################################################################################
+
+is_valid_client () {
+  local e match="$1"
+  shift
+  for e; do [[ "$e" == "$match" ]] && return 0; done
+  return 1
+}
+
+# Test if client is valid
+
+clients=("google-storage" "registry" "globus" "dropbox" "google-drive")
+
+if [ "${cli}" != "" ]; then
+    is_valid_client "${cli}" "${clients[@]}"
+    if [ $? -ne 0 ]; then
+        echo "${cli} is not a valid choice! Choose from ${clients[@]}";
+        exit 1
+    fi
+    echo "Storage Client: ${cli}"
+else
+    echo "Storage Client: none"
+fi
+
+
+################################################################################
+### Build! #####################################################################
+################################################################################
+
+# Continue if the image recipe is found
+
+if [ -f "$recipe" ]; then
+
+    imagefile="`basename ${recipe} .def`.sif"
+
+    echo "Creating $imagefile using $recipe..."
+    singularity build $imagefile $recipe
+
+    # If the image is successfully built, test it and upload (examples)
+  
+    if [ -f "${imagefile}" ]; then
+
+        # Example testing using run (you could also use test command)
+
+        echo "Testing the image... Marco!"
+        singularity exec $imagefile echo "Polo!"
+
+        # Example sregistry commands to push to endpoints
+
+        if [ "${cli}" != "" ]; then
+
+            # If the uri isn't provided, he gets a robot name
+            if [ "${uri}" == "" ]; then
+                uri=$(python -c "from sregistry.logger.namer import RobotNamer; bot=RobotNamer(); print(bot.generate())")
+            fi
+
+            # If a tag is provided, add to uri
+            if [ "${tag}" != "" ]; then
+                uri="${uri}:${tag}"
+            fi
+
+            echo "Pushing ${uri} to ${cli}://"
+            echo "SREGISTRY_CLIENT=${cli} sregistry push --name ${uri} ${imagefile}"
+            SREGISTRY_CLIENT="${cli}" sregistry push --name "${uri}" "${imagefile}"
+
+        else
+            echo "Skipping upload. Image $imagefile is finished!"
+        fi
+
+    fi
+
+else
+
+    echo "Singularity recipe ${recipe} not found!"
+    exit 1
+
+fi

.gitlabci/setup.sh

+#!/bin/bash
+
+apt-get update && apt-get install -y wget git \
+                                          build-essential \
+                                          squashfs-tools \
+                                          libtool \
+                                          autotools-dev \
+                                          libarchive-dev \
+                                          automake \
+                                          autoconf \
+                                          uuid-dev \
+                                          libssl-dev \
+                                          python-pip
+
+
+## Somehow sed cant find /etc/sudoers
+#sed -i -e 's/^Defaults\tsecure_path.*$//' /etc/sudoers
+
+# Check Python
+
+echo "Python Version:"
+python --version
+pip install sregistry[all]
+sregistry version
+
+echo "sregistry Version:"
+
+# Install Singularity
+
+cd /tmp && \
+    rm -rf singularity && \
+    git clone -b vault/release-2.5 https://www.github.com/sylabs/singularity.git
+    cd singularity && \
+    ./autogen.sh && \
+    ./configure --prefix=/usr/local && \
+    make -j8 && make install

CMakeLists.txt

+## CMake project file for hallac_container
+
+################################################################################
+## PROJECT: hallac_container
+################################################################################
+cmake_minimum_required (VERSION 3.8)
+project (eic_container VERSION 1.6.7)
+
+################################################################################
+## The name of our container
+################################################################################
+set(CONTAINER eic-${PROJECT_VERSION}.sif)
+
+################################################################################
+## CMAKE Settings 
+################################################################################
+include(cmake/options.cmake)
+
+################################################################################
+## Subdirectories
+################################################################################
+
+add_subdirectory(containers)
+add_subdirectory(modulefiles)
+add_subdirectory(scripts)

README.md

+EIC software container
+============================================
+
+Installation
+-----------
+
+1. Checkout the repository and create a build directory
+```
+git clone https://eicweb.phy.anl.gov/containers/eic_containers.git
+cd eic_containers && mkdir BUILD && cd BUILD
+```
+
+2. Configure the install for your environment, providing the appropriate `prefix` and
+   `module_dir` you want to use.
+```
+cmake .. -DCMAKE_INSTALL_PREFIX=<prefix> -DINSTALL_MODULE_DIR=<module_dir>
+```
+
+3. Download the container and install.
+```
+make install
+```
+
+4. To use the container: load the modulefile, and then use the included apps as if
+   they are native to your system!
+```
+module load eic_container
+```
+

cmake/options.cmake

+################################################################################
+## CMAKE Settings 
+################################################################################
+## make sure that the default is RELEASE
+if (NOT CMAKE_BUILD_TYPE)
+  set (CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING
+      "Choose the type of build, options are: None Debug Release RelWithDebInfo."
+      FORCE)
+endif ()
+## Offer the user the choice of overriding the installation directories
+set(INSTALL_LIB_DIR lib CACHE PATH "Installation directory for libraries")
+set(INSTALL_BIN_DIR bin CACHE PATH "Installation directory for executables")
+set(INSTALL_INCLUDE_DIR include/${PROJECT_NAME} CACHE PATH "Installation directory for header files")
+set(INSTALL_MODULE_DIR ${CMAKE_INSTALL_PREFIX}/../../etc/modulefiles CACHE PATH "Installation directory for module files")
+set(INSTALL_BIND_PATH "/net" "/group" "/cache" "/work" "/volatile" CACHE PATH "Installation singularity bind path")
+if(WIN32 AND NOT CYGWIN)
+  set(DEF_INSTALL_CMAKE_DIR cmake)
+else()
+  set(DEF_INSTALL_CMAKE_DIR lib/cmake/${PROJECT_NAME})
+endif()
+set(INSTALL_CMAKE_DIR ${DEF_INSTALL_CMAKE_DIR} CACHE PATH
+  "Installation directory for cmake files")
+## Make relative paths absolute (useful when auto-generating cmake configuration
+## files) Note: not including INSTALL_BIND_PATH on purpose as we should be giving absolute
+## paths anyway
+foreach(p LIB BIN INCLUDE CMAKE MODULE)
+  set(var INSTALL_${p}_DIR)
+  if(NOT IS_ABSOLUTE "${${var}}")
+    set(${var} "${CMAKE_INSTALL_PREFIX}/${${var}}")
+  endif()
+endforeach()
+## extra cmake modules
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} 
+  "${PROJECT_SOURCE_DIR}/cmake/")

containers/CMakeLists.txt

+################################################################################
+## Download the container
+################################################################################
+
+set(CONTAINER_SOURCE
+  "https://eicweb.phy.anl.gov/containers/eic_container/-/jobs/artifacts/v${PROJECT_VERSION}/raw/build/eic.sif?job=eic_singularity")
+
+add_custom_command(OUTPUT ${CONTAINER} 
+  COMMAND wget ${CONTAINER_SOURCE} -O ${CONTAINER}
+  COMMENT "Downloading ${CONTAINER}"
+)
+
+################################################################################
+## Global target
+################################################################################
+add_custom_target(container ALL 
+  DEPENDS ${CONTAINER})
+
+################################################################################
+## Install the container to <prefix>/lib
+################################################################################
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${CONTAINER}
+  DESTINATION "${INSTALL_LIB_DIR}" COMPONENT lib)

containers/docker/Dockerfile

+FROM  eicweb.phy.anl.gov:4567/containers/image_recipes/dd4hep_base:latest
+
+LABEL maintainer="Whitney Armstrong <warmstrong@anl.gov>" \
+      name="eic_container" \
+      group="containers/eic_containers" \
+      march="native" \
+      basedist="ubuntu" \
+      base="dd4hep_base"
+
+
+ENV EPICS_ROOT="/usr/local/epics"                                         \
+    EPICS_BASE="/usr/local/epics/base"                                     \
+    PYTHONPATH="/usr/local/lib:${PYTHONPATH}"                              \
+    EPICS_HOST_ARCH="linux-x86_64"                                         \
+    PATH="${EPICS_ROOT}/bin:${EPICS_ROOT}/bin/${EPICS_HOST_ARCH}:${PATH}:" \
+    LD_LIBRARY_PATH="${EPICS_ROOT}/lib:${EPICS_BASE}/bin/${EPICS_HOST_ARCH}:${LD_LIBRARY_PATH}"
+
+#RUN source /usr/local/bin/thisroot.sh                                                     \
+#      && echo "  -------------------------------------------------"                            \
+#      && echo "  0. Installing project dependencies"                                           \
+#      && echo "  -------------------------------------------------"                            \
+#      && apt-get install libtbb-dev libtbb2                                                    \
+#      && sed -i 's/\/tmp\/builds\/root_build\/lib\/libtbb.so/\/usr\/local\/lib\/libtbb.so/g'   \
+#          /usr/local/cmake/ROOTConfig-targets.cmake                                             \
+#      && echo "  -------------------------------------------------"                                \
+#      && echo "  1. Installing project library: libfmt"                                            \
+#      && echo "  -------------------------------------------------"                                \
+#      && echo " spdlog now in base image"
+#
+#RUN echo "  -------------------------------------------------"                      \
+#  && echo "  2. Installing project library: nlohmann/json"                             \
+#  && echo "  -------------------------------------------------"                        \
+#  && source /usr/local/bin/thisroot.sh                                                 \
+#  && echo "  -------------------------------------------------"                        \
+#  && echo "  3. Installing: eic/EVIO"                                               \
+#  && echo "  -------------------------------------------------"                        \
+#  && cd /tmp                                                                           \
+#  && git clone https://eicweb.phy.anl.gov/jlab/hallc/analyzer_software/eic_evio.git \
+#  && cd eic_evio && git checkout v4.4.6                                          \
+#  && mkdir build && cd build                                                        \
+#  && cmake ../.  && make -j20 && make install                                       \
+#  && cd /tmp && rm -rf eic_evio                                                     \
+#  && echo "  -------------------------------------------------"                        \
+#  && echo "  4. Installing: Coda/ET"                                                   \
+#  && echo "  -------------------------------------------------"                        \
+#  && cd /tmp                                                                           \
+#  && git clone https://eicweb.phy.anl.gov/jlab/coda/et.git                             \
+#  && cd et && git checkout v12.0.1                                                \
+#  && mkdir build && cd build                                                      \
+#  && cmake ../. -DINSTALL_LMOD_FILES=OFF && make -j20 && make install             \
+#  && cd /tmp && rm -rf et
+#
+#RUN echo "  -------------------------------------------------"                        \
+#  && echo "  5. Installing: Podd"                                                      \
+#  && echo "  -------------------------------------------------"                        \
+#  && cd /tmp                                                                           \
+#  && ls -lrth /usr/local/lib/cmake/* \
+#  && ls -lrth /usr/local/lib/cmake/spdlog * \
+#  && git clone https://eicweb.phy.anl.gov/jlab/hallc/analyzer_software/analyzer.git    \
+#  && cd analyzer && git checkout v1.8.2                                           \
+#  && mkdir build && cd build                                                      \
+#  && cmake ../.  && make -j20 && make install                                     \
+#  && cd /tmp  && rm -rf analyzer
+#
+#RUN echo "  -------------------------------------------------"                            \
+#  && echo "  6. Installing: hcana"                                                           \
+#  && echo "  -------------------------------------------------"                              \
+#  && source /usr/local/bin/thisroot.sh                                                 \
+#  && cd /tmp && rm -rf hcana                                                                 \
+#  && git clone https://eicweb.phy.anl.gov/jlab/hallc/analyzer_software/hcana.git             \
+#  && cd hcana && git checkout v1.2.0                                                    \
+#  && mkdir build && cd build                                                            \
+#  && cmake ../.  && make -j20 && make install                                           \
+#  && cd /tmp && rm -rf hcana                                                                 \
+#  && echo "  -------------------------------------------------"                              \
+#  && echo "  7. Installing: hconline"                                                        \
+#  && echo "  -------------------------------------------------"                              \
+#  && cd /tmp && rm -rf hconline                                                              \
+#  && git clone https://eicweb.phy.anl.gov/jlab/hallc/analyzer_software/hconline.git          \
+#  && cd hconline && git checkout v1.1.7                                                 \
+#  && mkdir build && cd build                                                            \
+#  && cmake ../.  && make -j20 && make install                                           \
+#  && cd /tmp && rm -rf hconline
+#
+#RUN  cd /tmp \
+#  && echo "  -------------------------------------------------"                              \
+#  && echo "  8. Installing: hallc_tools"                                                     \
+#  && echo "  -------------------------------------------------"                              \
+#  && cd /tmp \
+#  && git clone --depth=1 --branch 0.9.1 https://github.com/ericniebler/range-v3.git \
+#  && mkdir -p range-v3/build && cd range-v3/build \
+#  && cmake ../. -DRANGE_V3_PERF=OFF -DRANGE_BUILD_CALENDAR_EXAMPLE=OFF \
+#  -DBUILD_TESTING=OFF -DRANGE_V3_EXAMPLES=OFF \
+#  -DRANGE_V3_TESTS=OFF -DRANGE_V3_DOCS=OFF \
+#  -DRANGES_CXX_STD=17    \
+#  && make -j8 install \
+#  && cd /tmp && rm -r range-v3 \
+#  && git clone https://eicweb.phy.anl.gov/jlab/hallc/analyzer_software/hallc_tools.git       \
+#  && cd hallc_tools && git checkout v1.1.9                                                   \
+#  && mkdir build && cd build                                                                 \
+#  && cmake ../.  && make -j20 && make install                                                \
+#  && cd /tmp && rm -rf hallc_tools                                                           \ 
+#  && echo "  -------------------------------------------------"                              \
+#  && echo "  10. Slimming down image"                                                        \
+#  && echo "  -------------------------------------------------"                              \
+#  && apt-get clean                                                                           \
+#  && rm -rf /var/lib/apt/lists/*                                                             \
+#  && echo "  -------------------------------------------------"                              
+#
+##  && echo "  9. Installing: simc"                                                           \
+##  && echo "  -------------------------------------------------"                             \
+##  && cd /tmp
+##  git clone --recurse-submodules https://eicweb.phy.anl.gov/jlab/hallc/simulation/simc-file-input.git \
+##    && cd simc-file-input && git checkout v1.0.0 && cd -                                               \
+##    mkdir build && cd build && cmake ../simc-file-input && make -j4 install                            \
+##  cd /tmp && rm -rf build simc-file-input                                                              \
+##  echo "  -------------------------------------------------"                                           \
+##  echo "  ===> Image setup complete"                                                                   \
+##  echo "  -------------------------------------------------"                                           \

containers/docker/config.env

+REG_TOKEN ?= ${CI_IMAGE_BUILD_PAT}
+REG_USER  ?= whit
+REG_HOST  ?= eicweb.phy.anl.gov
+REG_NAME  ?= eicweb.phy.anl.gov:4567
+REG_PORT  ?= 4567
+REG_URL   ?= https://$(REG_HOST)
+
+# name of alternate build: 
+# Dockerfile.$(ALT_NAME) --> $(APP_NAME)_${ALT_NAME}
+ALT_NAME ?= broadwell
+
+APP_NAME     = eic_container
+REPO_NAME    = eic_container
+
+DH_ORG       = eic
+
+GL_GROUP     = eic_container
+GL_REG_GROUP = containers/eic_container
+GL_REG_NAME  = $(REG_NAME)
+
+REPO         = $(REG_USER)
+TAG_VERSION  = latest

containers/docker/usage.sh

+# INSTALL
+# - copy the files deploy.env, config.env, version.sh and Makefile to your repo
+# - replace the vars in deploy.env
+# - define the version script
+
+# Build the container
+make build
+
+# Build and publish the container
+make release
+
+# Publish a container to AWS-ECR.
+# This includes the login to the repo
+make publish
+
+# Run the container
+make run
+
+# Build an run the container
+make up
+
+# Stop the running container
+make stop
+
+# Build the container with differnt config and deploy file
+make cnf=another_config.env dpl=another_deploy.env build
\ No newline at end of file

containers/docker/version.sh

+#!/bin/bash
+
+grep "hallac_container VERSION" ../../CMakeLists.txt | sed 's/project (hallac_container VERSION //' | sed 's/)//'
+

containers/singularity/eic.def

+Bootstrap: docker
+From: eicweb.phy.anl.gov:4567/containers/eic_container/eic_container:latest
+
+%help
+  EIC software container.
+  Tools:
+     - root        : root version used for the analyzer
+     - rootls, rootbrowse, root-config, hadd, h2root
+     - dd4hep
+
+%labels
+  Maintainer "Whitney Armstrong"
+  Version v1.0
+
+%post -c /bin/bash
+  #export PYTHONPATH=/usr/local/lib:$PYTHONPATH  
+  #export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
+  #export PATH=/usr/local/bin:$PATH  
+  #source /usr/local/bin/thisroot.sh 
+  #echo "  -------------------------------------------------"
+  #echo "  0. Installing project dependencies"
+  #echo "  -------------------------------------------------"
+  #apt-get install libtbb-dev libtbb2
+  ### this line fixes the ROOT cmake TBB bug
+  #sed -i 's/\/tmp\/builds\/root_build\/lib\/libtbb.so/\/usr\/local\/lib\/libtbb.so/g' /usr/local/cmake/ROOTConfig-targets.cmake
+  #export EPICS_ROOT=/usr/local/epics
+  #export EPICS_BASE=/usr/local/epics/base
+  #export EPICS_HOST_ARCH=linux-x86_64
+  #export PATH=$EPICS_ROOT/bin:$PATH
+  #export LD_LIBRARY_PATH=$EPICS_ROOT/lib:$LD_LIBRARY_PATH
+  #export PATH=$EPICS_BASE/bin/$EPICS_HOST_ARCH:$PATH
+  #export LD_LIBRARY_PATH=$EPICS_BASE/lib/$EPICS_HOST_ARCH:$LD_LIBRARY_PATH
+  #echo "  -------------------------------------------------"
+  #echo "  1. Installing project library: libfmt"
+  #echo "  -------------------------------------------------"
+  #cd /tmp
+  #git clone https://github.com/fmtlib/fmt.git && cd fmt && \
+  #  git checkout 5.3.0 && mkdir /tmp/build && cd /tmp/build && \
+  #  cmake -DBUILD_SHARED_LIBS=TRUE ../fmt &&
+  #  make -j20 install 
+  #cd /tmp && rm -r /tmp/build && rm -r /tmp/fmt
+  #echo "  -------------------------------------------------"
+  #echo "  2. Installing project library: nlohmann/json"
+  #echo "  -------------------------------------------------"
+  #apt-get install nlohmann-json-dev
+  #echo "  -------------------------------------------------"
+  #echo "  3. Installing: eic/EVIO"
+  #echo "  -------------------------------------------------"
+  #cd /tmp
+  #git clone https://eicweb.phy.anl.gov/jlab/hallc/analyzer_software/eic_evio.git \
+  #  && cd eic_evio && git checkout v4.4.6 \
+  #  && mkdir build && cd build  \
+  #  && cmake ../.  && make -j20 && make install
+  #cd /tmp && rm -rf eic_evio
+  #echo "  -------------------------------------------------"
+  #echo "  4. Installing: Coda/ET"
+  #echo "  -------------------------------------------------"
+  #cd /tmp
+  #git clone https://eicweb.phy.anl.gov/jlab/coda/et.git \
+  #  && cd et && git checkout v12.0.1 \
+  #  && mkdir build && cd build  \
+  #  && cmake ../. -DINSTALL_LMOD_FILES=OFF && make -j20 && make install
+  #cd /tmp && rm -rf et
+  #echo "  -------------------------------------------------"
+  #echo "  5. Installing: Podd"
+  #echo "  -------------------------------------------------"
+  #cd /tmp 
+  #git clone https://eicweb.phy.anl.gov/jlab/hallc/analyzer_software/analyzer.git \
+  #  && cd analyzer && git checkout v1.8.2 \
+  #  && mkdir build && cd build \
+  #  && cmake ../.  && make -j20 && make install 
+  #cd /tmp  && rm -rf analyzer
+  #echo "  -------------------------------------------------"
+  #echo "  6. Installing: hcana"
+  #echo "  -------------------------------------------------"
+  #cd /tmp && rm -rf hcana
+  #git clone https://eicweb.phy.anl.gov/jlab/hallc/analyzer_software/hcana.git \
+  #  && cd hcana && git checkout v1.1.9 \
+  #  && mkdir build && cd build  \
+  #  && cmake ../.  && make -j20 && make install
+  #cd /tmp && rm -rf hcana 
+  #echo "  -------------------------------------------------"
+  #echo "  7. Installing: hconline"
+  #echo "  -------------------------------------------------"
+  #cd /tmp && rm -rf hconline
+  #git clone https://eicweb.phy.anl.gov/jlab/hallc/analyzer_software/hconline.git \
+  #  && cd hconline && git checkout v1.1.5 \
+  #  && mkdir build && cd build  \
+  #  && cmake ../.  && make -j20 && make install
+  #cd /tmp && rm -rf hconline 
+  #echo "  -------------------------------------------------"
+  #echo "  8. Installing: hallc_tools"
+  #echo "  -------------------------------------------------"
+  #cd /tmp && rm -rf hallc_tools
+  #git clone https://eicweb.phy.anl.gov/jlab/hallc/analyzer_software/hallc_tools.git \
+  #  && cd hallc_tools && git checkout v1.0.0 \
+  #  && mkdir build && cd build  \
+  #  && cmake ../.  && make -j20 && make install
+  #cd /tmp && rm -rf hallc_tools 
+  #echo "  -------------------------------------------------"
+  #echo "  9. Installing: simc"
+  #echo "  -------------------------------------------------"
+  #cd /tmp
+  #git clone --recurse-submodules https://eicweb.phy.anl.gov/jlab/hallc/simulation/simc-file-input.git \
+  #  && cd simc-file-input && git checkout v1.0.0 && cd - \
+  #  mkdir build && cd build && cmake ../simc-file-input && make -j4 install
+  #cd /tmp && rm -rf build simc-file-input
+  #echo "  -------------------------------------------------"
+  #echo "  10. Slimming down image"
+  #echo "  -------------------------------------------------"
+  #apt-get clean
+  #rm -rf /var/lib/apt/lists/*
+  echo " Image build is now mostly done in dockerfile"
+  echo "  -------------------------------------------------"
+  echo "  ===> Image setup complete"
+  echo "  -------------------------------------------------"
+
+# ===================================
+# GLOBAL
+# ===================================
+
+%environment -c /bin/bash
+  export PYTHONPATH=/usr/local/lib:$PYTHONPATH
+  export PATH=/usr/loca/bin:${PATH}
+  export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
+  export ROOT_INCLUDE_PATH=/usr/local/include
+  export EPICS_ROOT=/usr/local/epics
+  export EPICS_BASE=/usr/local/epics/base
+  export EPICS_HOST_ARCH=linux-x86_64
+  export PATH=$EPICS_ROOT/bin:$PATH
+  export LD_LIBRARY_PATH=$EPICS_ROOT/lib:$LD_LIBRARY_PATH
+  export PATH=$EPICS_BASE/bin/$EPICS_HOST_ARCH:$PATH
+  export LD_LIBRARY_PATH=$EPICS_BASE/lib/$EPICS_HOST_ARCH:$LD_LIBRARY_PATH
+
+%runscript
+  echo "Launching a shell in the Hall A/C container."
+  echo "Use through singularity apps recommended (see help for more info)."
+  exec bash
+
+# ===================================
+# SIMC
+# ===================================
+%apprun simc
+  simc "%@"
+
+%appenv simc
+  export PYTHONPATH=/usr/local/lib:$PYTHONPATH
+  export PATH=/usr/loca/bin:${PATH}
+  export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
+  export ROOT_INCLUDE_PATH=/usr/local/include
+
+# =======================
+# root
+# =======================
+%apprun root
+  root "$@"
+
+%appenv root
+  export PYTHONPATH=/usr/local/lib:${PYTHONPATH}
+  export PATH=/usr/local/bin:${PATH}
+  export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
+  export ROOT_INCLUDE_PATH=/usr/local/include/podd:/usr/local/include/hcana
+  export EPICS_ROOT=/usr/local/epics
+  export EPICS_BASE=/usr/local/epics/base
+  export EPICS_HOST_ARCH=linux-x86_64
+  export PATH=$EPICS_ROOT/bin:$PATH
+  export LD_LIBRARY_PATH=$EPICS_ROOT/lib:$LD_LIBRARY_PATH
+  export PATH=$EPICS_BASE/bin/$EPICS_HOST_ARCH:$PATH
+  export LD_LIBRARY_PATH=$EPICS_BASE/lib/$EPICS_HOST_ARCH:$LD_LIBRARY_PATH
+
+# =======================
+# analyzer
+# =======================
+%apprun analyzer
+  analyzer "$@"
+
+%appenv analyzer
+  export PYTHONPATH=/usr/local/lib:${PYTHONPATH}
+  export PATH=/usr/local/bin:${PATH}
+  export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
+  export ROOT_INCLUDE_PATH=/usr/local/include/podd:/usr/local/include/hcana
+  export EPICS_ROOT=/usr/local/epics
+  export EPICS_BASE=/usr/local/epics/base
+  export EPICS_HOST_ARCH=linux-x86_64
+  export PATH=$EPICS_ROOT/bin:$PATH
+  export LD_LIBRARY_PATH=$EPICS_ROOT/lib:$LD_LIBRARY_PATH
+  export PATH=$EPICS_BASE/bin/$EPICS_HOST_ARCH:$PATH
+  export LD_LIBRARY_PATH=$EPICS_BASE/lib/$EPICS_HOST_ARCH:$LD_LIBRARY_PATH
+
+# =======================
+# hcana
+# =======================
+%apphelp hcana
+  Run the Hall-C analyzer with same root-style arguments.
+
+%apprun hcana
+  hcana "$@"
+
+%appenv hcana
+  export DB_DIR=DBASE
+  export PYTHONPATH=/usr/local/lib:${PYTHONPATH}
+  export PATH=/usr/local/bin:${PATH}
+  export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
+  export ROOTSYS=/usr/local
+  export ROOT_INCLUDE_PATH=/usr/local/include
+  export EPICS_ROOT=/usr/local/epics
+  export EPICS_BASE=/usr/local/epics/base
+  export EPICS_HOST_ARCH=linux-x86_64
+  export PATH=$EPICS_ROOT/bin:$PATH
+  export LD_LIBRARY_PATH=$EPICS_ROOT/lib:$LD_LIBRARY_PATH
+  export PATH=$EPICS_BASE/bin/$EPICS_HOST_ARCH:$PATH
+  export LD_LIBRARY_PATH=$EPICS_BASE/lib/$EPICS_HOST_ARCH:$LD_LIBRARY_PATH
+
+# =======================
+# root-config
+# =======================
+%apprun root-config
+  root-config "$@"
+
+%appenv root-config
+  export PYTHONPATH=/usr/local/lib:${PYTHONPATH}
+  export PATH=/usr/local/bin:${PATH}
+  export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
+  export ROOT_INCLUDE_PATH=/usr/local/include/podd:/usr/local/include/hcana
+
+
+# =======================
+# rootbrowse
+# =======================
+%apprun rootbrowse
+  rootbrowse "$@"
+
+%appenv rootbrowse
+  export PYTHONPATH=/usr/local/lib:${PYTHONPATH}
+  export PATH=/usr/local/bin:${PATH}
+  export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
+  export ROOT_INCLUDE_PATH=/usr/local/include/podd:/usr/local/include/hcana
+
+# =======================
+# rootls
+# =======================
+%apprun rootls
+  rootls "$@"
+
+%appenv rootls
+  export PYTHONPATH=/usr/local/lib:${PYTHONPATH}
+  export PATH=/usr/local/bin:${PATH}
+  export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
+  export ROOT_INCLUDE_PATH=/usr/local/include/podd:/usr/local/include/hcana
+
+# =======================
+# hadd
+# =======================
+%apprun hadd
+  hadd "$@"
+
+%appenv hadd
+  export PYTHONPATH=/usr/local/lib:${PYTHONPATH}
+  export PATH=/usr/local/bin:${PATH}
+  export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
+  export ROOT_INCLUDE_PATH=/usr/local/include/podd:/usr/local/include/hcana
+
+# =======================
+# h2root
+# =======================
+%apprun h2root
+  h2root "$@"
+
+%appenv h2root
+  export PYTHONPATH=/usr/local/lib:${PYTHONPATH}
+  export PATH=/usr/local/bin:${PATH}
+  export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
+  export ROOT_INCLUDE_PATH=/usr/local/include/podd:/usr/local/include/hcana
+
+# =======================
+# xml2evio
+# =======================
+%apprun xml2evio
+  xml2evio "$@"
+
+%appenv xml2evio
+  export PYTHONPATH=/usr/local/lib:${PYTHONPATH}
+  export PATH=/usr/local/bin:${PATH}
+  export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
+  export ROOT_INCLUDE_PATH=/usr/local/include/podd:/usr/local/include/hcana
+
+# =======================
+# evio2xml
+# =======================
+%apprun evio2xml
+  evio2xml "$@"
+
+%appenv evio2xml
+  export PYTHONPATH=/usr/local/lib:${PYTHONPATH}
+  export PATH=/usr/local/bin:${PATH}
+  export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
+  export ROOT_INCLUDE_PATH=/usr/local/include/podd:/usr/local/include/hcana
+
+# =======================
+# evioCat
+# =======================
+%apprun evioCat
+  evioCat "$@"
+
+%appenv evioCat
+  export PYTHONPATH=/usr/local/lib:${PYTHONPATH}
+  export PATH=/usr/local/bin:${PATH}
+  export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
+  export ROOT_INCLUDE_PATH=/usr/local/include/podd:/usr/local/include/hcana
+
+# =======================
+# eviocopy
+# =======================
+%apprun eviocopy
+  eviocopy "$@"
+
+%appenv eviocopy
+  export PYTHONPATH=/usr/local/lib:${PYTHONPATH}
+  export PATH=/usr/local/bin:${PATH}
+  export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
+  export ROOT_INCLUDE_PATH=/usr/local/include/podd:/usr/local/include/hcana

modulefiles/CMakeLists.txt

+################################################################################
+## Configure modulefile for our environment
+################################################################################
+set(MODULEFILE "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH}")
+configure_file(modulefile.in ${MODULEFILE} @ONLY)
+
+################################################################################
+## Install the modulefile to <install_module_dir>/<project>/<version>
+################################################################################
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${MODULEFILE}
+  DESTINATION "${INSTALL_MODULE_DIR}/${PROJECT_NAME}" COMPONENT lib)

modulefiles/modulefile.in

+#%Module1.0#####################################################################
+##
+## for tmux
+##
+proc ModulesHelp { } {
+    puts stderr "This module sets up the environment for the EIC container"
+}
+module-whatis   "@PROJECT_NAME@ @PROJECT_VERSION_MAJOR@.@PROJECT_VERSION_MINOR@"
+
+# for Tcl script use only
+set    version        4.1.4
+set iprefix @CMAKE_INSTALL_PREFIX@
+
+prepend-path    PATH             $iprefix/bin

scripts/CMakeLists.txt

+################################################################################
+## Configure launcher scripts for our singularity apps
+################################################################################
+
+set(APPS 
+  "analyzer"
+  "evio2xml"
+  "evioCat"
+  "eviocopy"
+  "hcana"
+  "root"
+  "root-config"
+  "rootbrowse"
+  "rootls"
+  "xml2evio" 
+  "et_feeder" 
+  "et_consumer" 
+  "et_producer"
+  "hc_display_server"
+  "hc_spec"
+  "softIoc"
+  "softIocPVA"
+  "caget"
+  "caput"
+  "pvput"
+  "pvget"
+  "camonitor"
+  "pvmonitor"
+  "mongo"
+  "mongod"
+  "mongodump"
+  "mongoexport"
+  "mongoimport"
+  "mongostat"
+  )
+
+set(APPS_ABSOLUTE_PATH "")
+
+## Bind directive for known systems
+set (OPT_BIND_DIRECTIVE "")
+foreach(BIND_PATH ${INSTALL_BIND_PATH})
+  if (NOT "${BIND_PATH} " EQUAL " " AND EXISTS ${BIND_PATH})
+    set (OPT_BIND_DIRECTIVE "${OPT_BIND_DIRECTIVE} -B ${BIND_PATH}:${BIND_PATH} ")
+  endif ()
+endforeach()
+message("Adding singularity bind directive: '${OPT_BIND_DIRECTIVE}'")
+
+find_program(SINGULARITY singularity)
+
+foreach(APP ${APPS})
+  configure_file(launcher.in ${APP} @ONLY)
+  set(APPS_ABSOLUTE_PATH ${APPS_ABSOLUTE_PATH} "${CMAKE_CURRENT_BINARY_DIR}/${APP}")
+endforeach ()
+
+################################################################################
+## Install the launcher scripts to <prefix>/bin
+################################################################################
+install(PROGRAMS ${APPS_ABSOLUTE_PATH}
+  DESTINATION "${INSTALL_BIN_DIR}" COMPONENT bin)

scripts/launcher.in

+#!/bin/bash
+
+piped_args=
+if [ -p /dev/stdin ]; then
+  # If we want to read the input line by line
+  while IFS= read line; do
+    #echo "Line: ${line}"
+    if [ -z "$piped_args" ]; then
+      piped_args="${line}"
+    else 
+      piped_args="${piped_args}\n${line}"
+    fi
+  done
+fi
+
+if [ ${piped_args} ]  ; then
+echo -e ${piped_args} | @SINGULARITY@ exec @OPT_BIND_DIRECTIVE@@INSTALL_LIB_DIR@/@CONTAINER@ @APP@ $@
+else
+@SINGULARITY@ exec @OPT_BIND_DIRECTIVE@@INSTALL_LIB_DIR@/@CONTAINER@ @APP@ $@
+fi