diff --git a/requirements.txt b/requirements.txt
index 186ea552d..f8ead20aa 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,26 +1,14 @@
-astroplan
-astropy >= 3.0.0
-ccdproc
-codecov
-coveralls
-dateparser
+# These are packages that are NOT available via our
+# choice of conda repositories; there are less well
+# known repositories that do offer them, but that is
+# more of a security risk.
+
+# Thin Python wrapper for ffmpeg. We *could* replace with our own wrapper.
 ffmpy
-gcloud
-google-cloud-storage
-matplotlib >= 2.0.0
+
+# Mock object support for Python testing.
 mocket
-numpy >= 1.12.1
-pycodestyle == 2.3.1
-pymongo >= 3.2.2
-pyserial >= 3.1.1
-pytest >= 3.4.0
-python_dateutil >= 2.5.3
-PyYAML >= 3.11
-pyzmq >= 15.3.0
-readline
-requests
-scikit_image >= 0.12.3
-scipy >= 0.17.1
+
+# State machine library for Python.
 transitions >= 0.4.0
-tweepy
-wcsaxes
+
diff --git a/scripts/install/apt-packages-list.txt b/scripts/install/apt-packages-list.txt
index 556a02e9a..df9d12926 100644
--- a/scripts/install/apt-packages-list.txt
+++ b/scripts/install/apt-packages-list.txt
@@ -2,7 +2,8 @@
 # Lines starting with # are comments as are blank lines,
 # and # starts trailing comments.
 
-# dcraw decodes Canon raw images
+# dcraw decodes Canon raw images. See also libraw.org for an alternate source
+# of the underlying algorithms. Neither has an up-to-date conda package.
 dcraw
 
 # gphoto2 enables remote control of cameras, including the Canon DSLRs that
@@ -11,31 +12,34 @@ dcraw
 # old relative to the latest stable version. gphoto2-updater is an install
 # script that we might want to use if we need a newer version. For more info,
 # see: https://github.com/gonzalo/gphoto2-updater
+# There is an old conda package.
 gphoto2
 
 # Packages needed according to http://astrometry.net/doc/build.html
-libbz2-dev
-libbz2-dev
-libcfitsio-dev
-libjpeg-dev
-libnetpbm10-dev
-libpng12-dev
-netpbm
-python-dev
-python-numpy
-python-pyfits
-swig
-zlib1g-dev
-
-# Cairo is a graphics library, and matplotlib can use it as a backend
-# for rendering.
-libcairo2-dev 
-
-# exiftool is used in a couple of places to extract info from the .cr2 file
-exiftool 
+libbz2-dev        # Not available in our conda repos.
+libcfitsio-dev    # Probably already satisfied in conda.
+libjpeg-dev       # Conda has libjpeg-turbo, apparently the same API but faster.
+libnetpbm10-dev   # Used for making pretty pictures of solutions.
+libpng-dev        # Used for making pretty pictures of solutions. ALREADY installed by conda.
+netpbm            # Used for making pretty pictures of solutions.
+python-dev        # Probably already satisfied in conda.
+python-numpy      # Probably already satisfied in conda.
+python-pyfits     # Not available in our conda repos.
+swig              # Available from conda.
+zlib1g-dev        # Available from conda as zlib.
+
+# Cairo is a 2D graphics library, and matplotlib can use it as a backend
+# for rendering, and used by astrometry for pretty pictures of solutions.
+# Stable, but not latest, version available from conda.
+libcairo2-dev
+
+# exiftool is used in a couple of places to extract info from the .cr2 file.
+# Consider using Python package exifread instead, which doesn't require exiftool
+exiftool
 
 # We use cfitsio command line tools (e.g. fpack) from POCS, in addition to the
 # uses of the cfitsio libraries by astrometry above.
+# 'conda install cfitsio' brings in fpack.
 libcfitsio-bin
 
 # These are used if you want to setup SSH access into the computer (pretty
@@ -44,6 +48,8 @@ openssh-client
 openssh-server
 
 # Graphviz is used for rendering the state machine of POCS.
+# Do we need both of these? Do we use the command-line tools in graphviz,
+# or just the pygraphviz library?
 graphviz
 libgraphviz-dev
 
@@ -51,9 +57,11 @@ libgraphviz-dev
 pkg-config
 
 # Improves interaction with pocs_shell (via readline).
+# Available from conda as ncurses.
 libncurses5-dev
 
 # These support the Python package "Shapely", used in PIAA (called from POCS).
+# Conda has geos 3.6. Not sure if this covers libgeos-c1v5 and libgeos-dev.
 libgeos-3.*
 libgeos-c1v5
 libgeos-dev
@@ -64,7 +72,14 @@ byobu
 tmux
 
 # Used for creating a timelapse.
+# Available from conda.
 ffmpeg
 
 # Used for colorizing log files.
 grc
+
+# https://jupyter.org/
+# Lots of jupyter packages available from conda, not sure whether this includes
+# jupyter-notebook features exactly as we need.
+jupyter-notebook
+
diff --git a/scripts/install/conda-packages-list.txt b/scripts/install/conda-packages-list.txt
index d820bb9bb..4e6ffc030 100644
--- a/scripts/install/conda-packages-list.txt
+++ b/scripts/install/conda-packages-list.txt
@@ -1,2 +1,38 @@
+# These are packages that we install with conda. They include both Python
+# packages and non-Python libraries on which we depend (usually via a
+# Python package depending on some native code).
+
+astroplan
+astropy >= 3.0.0
+ccdproc
+cfitsio   # This is an experiment. Requires adjusting apt-packages-list.
+codecov
+coveralls
+cython
+dateparser
+google-cloud-sdk
+google-cloud-storage
+matplotlib >= 2.0.0
+numpy >= 1.12.1
+pycodestyle == 2.3.1
+pymongo >= 3.2.2
+pyserial >= 3.1.1
+pytest >= 3.4.0
 pandas
+python
+python-dateutil >= 2.5.3
+PyYAML >= 3.11
+pyzmq >= 15.3.0
+readline
+requests
+scikit-image >= 0.12.3
+scipy >= 0.17.1
+
+# Jupyter-notebook requires Tornado versions between 4 and 5. See:
+# https://stackoverflow.com/questions/49141525/install-jupyter-notebook-on-miniconda
+# https://github.com/ipython/ipython/issues/8249
+# https://github.com/jupyter/help/issues/324
 
+tornado == 4.5.3
+tweepy
+wcsaxes
diff --git a/scripts/install/install-dependencies.sh b/scripts/install/install-dependencies.sh
index d95f562de..080799f14 100755
--- a/scripts/install/install-dependencies.sh
+++ b/scripts/install/install-dependencies.sh
@@ -1,5 +1,8 @@
 #!/bin/bash -e
 
+# Run with --help to see your options. With no options, does a complete install
+# of dependencies, though attempts to reuse existing installs.
+
 THIS_DIR="$(dirname $(readlink -f "${0}"))"
 THIS_PROGRAM="$(basename "${0}")"
 
@@ -12,8 +15,6 @@ fi
 mkdir -p "${PANDIR}"
 cd "${PANDIR}"
 
-# TODO(jamessynge): Add flags to control behavior, such as skipping apt-get.
-
 ASTROMETRY_VERSION="0.72"
 INSTALL_PREFIX="/usr/local"
 
@@ -27,40 +28,88 @@ DO_ASTROMETRY=1
 DO_ASTROMETRY_INDICES=1
 DO_PIP_REQUIREMENTS=1
 
+# Which bash file do we need to modify? The last found here is the one that
+# bash executes for login shells, and so provides the environment for
+# all processes under that.
+THE_PROFILE="${HOME}/.profile"
+if [[ -f "${HOME}/.bash_login" ]] ; then
+  THE_PROFILE="${HOME}/.bash_login"
+fi
+if [[ -f "${HOME}/.bash_profile" ]] ; then
+  THE_PROFILE="${HOME}/.bash_profile"
+fi
+
 function echo_bar() {
-  eval $(resize|grep COLUMNS=)
+  if [[ -n "$(which resize)" ]] ; then
+    eval $(resize|grep COLUMNS=)
+  elif [[ -n "$(which stty)" ]] ; then
+    COLUMNS="$(stty size | cut '-d ' -f2)"
+  fi
   printf "%${COLUMNS:-80}s\n" | tr ' ' '#'
 }
 
-# Append $1 to .profile 
-function add_to_profile() {
-  local -r the_line="${1}"
-  local -r the_file="${HOME}/.profile"
-  if [[ ! -f "${the_file}" ]] ; then
-    touch "${the_file}"
+function ensure_profile_exists() {
+  if [[ ! -f "${THE_PROFILE}" ]] ; then
+    touch "${THE_PROFILE}"
   fi
-  if [[ -z "$(fgrep -- "${the_line}" "${the_file}")" ]] ; then
-    echo >>"${the_file}" "
-# Added by PANOPTES install-dependencies.sh
-${the_line}"
-    echo "Appended to ${the_file}: ${the_line}"
+}
+
+function profile_contains_text() {
+  local -r target_text="${1}"
+  if [[ -n "$(fgrep -- "${target_text}" "${THE_PROFILE}")" ]] ; then
+    return 0
   else
-    echo "Already in ${the_file}: ${the_line}"
+    return 1
   fi
 }
 
+function add_to_profile_before_target() {
+  local -r new_text="${1}"
+  local -r target_text="${2}"
+  if profile_contains_text "${new_text}" ; then
+    echo "Already in ${THE_PROFILE}: ${new_text}"
+    return 0
+  fi
+  ensure_profile_exists
+  # This backup is just for debugging (i.e. showing the before and after
+  # diff).
+  local -r the_backup="$(mktemp "${THE_PROFILE}.pre-edit.XXXXX")"
+  cp -p "${THE_PROFILE}" "${the_backup}"
+  if profile_contains_text "${target_text}" ; then
+    # Add just before the target text.
+    sed -i "/${target_text}/i \
+# Added by PANOPTES install-dependencies.sh\n\
+${new_text}\n" "${THE_PROFILE}"
+  else
+    # Append to the end of the file.
+    echo >>"${THE_PROFILE}" "
+# Added by PANOPTES install-dependencies.sh
+${new_text}"
+  fi
+  # Again, this diff is just for debugging.
+  echo "Modified ${THE_PROFILE}:"
+  echo
+  diff -u "${the_backup}" "${THE_PROFILE}" || /bin/true
+  echo
+  rm "${the_backup}"
+}
+
+# Add $1 to .profile before where bashrc is invoked.
+# This assumes a standard (default) .profile.
+function add_to_profile_before_bashrc() {
+  add_to_profile_before_target "${1}" "# if running bash"
+}
+
 # Append $1 to PATH and write command to do the same to .profile.
 function add_to_PATH() {
   local -r the_dir="$(readlink -f "${1}")"
-  add_to_profile "PATH=\"${the_dir}:\${PATH}\""
+  add_to_profile_before_bashrc "PATH=\"${the_dir}:\${PATH}\""
   PATH="${the_dir}:${PATH}"
 
   return 0
 
   local -r the_file="${HOME}/.profile"
-  if [[ ! -f "${the_file}" ]] ; then
-    touch "${the_file}"
-  fi
+  ensure_profile_exists
   if [[ -z "$(egrep -- "PATH=.*${the_dir}" "${the_file}")" ]] ; then
     echo >>"${the_file}" "
 # Added by PANOPTES install-dependencies.sh
@@ -94,19 +143,47 @@ function install_apt_packages() {
 }
 
 function install_mongodb() {
-  # This is based on https://www.howtoforge.com/tutorial/install-mongodb-on-ubuntu-16.04/
+  # This is based on https://www.howtoforge.com/tutorial/install-mongodb-on-ubuntu/
   # Note this function does not configure mongodb itself, i.e. no users or
   # security settings.
   echo_bar
+  local MONGO_KEY=""
+  local MONGO_URL="http://repo.mongodb.org/apt/ubuntu"
+  local MONGO_VERSION=""
+  local MONGO_SOURCE_PATH=""
+  local LSB_RELEASE=""
+  if [[ -n "$(which lsb_release)" ]] ; then
+    LSB_RELEASE="$(lsb_release -sc)"
+  fi
+  if [[ "${LSB_RELEASE}" = "xenial" ]] ; then
+    MONGO_KEY=2930ADAE8CAF5059EE73BB4B58712A2291FA4AD5
+    MONGO_VERSION=3.6
+  elif [[ "${LSB_RELEASE}" = "bionic" ]] ; then
+    MONGO_KEY=9DA31620334BD75D9DCB49F368818C72E52529D4
+    MONGO_VERSION=4.0
+  else
+    echo "ERROR: don't know which version of MongoDB to install."
+    return 1
+  fi
+  MONGO_URL+=" ${LSB_RELEASE}/mongodb-org/${MONGO_VERSION}"
+  MONGO_SOURCE_PATH="/etc/apt/sources.list.d/mongodb-org-${MONGO_VERSION}.list"
+
   echo "
-Installing mongodb, for which several commands require sudo, so
-you may be prompted for you password.
+Installing MongoDB ${MONGO_VERSION}, for which several commands require sudo,
+so you may be prompted for you password. Starting by telling APT where to find
+the MongoDB packages.
+"
+  sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv ${MONGO_KEY}
+  echo "deb ${MONGO_URL} multiverse" | sudo tee "${MONGO_SOURCE_PATH}"
+  echo "
+Updating the list of packages so APT finds the MongoDB packages,
+then installing MongoDB.
 "
-  sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv EA312927
-  echo "deb http://repo.mongodb.org/apt/ubuntu "$(lsb_release -sc)"/mongodb-org/3.2 multiverse" \
-     | sudo tee /etc/apt/sources.list.d/mongodb-org-3.2.list
   sudo apt-get update
   sudo apt-get install -y mongodb-org
+  echo "
+MongoDB is installed, now updating the config and starting mongod.
+"
   echo "[Unit]
 Description=High-performance, schema-free document-oriented database
 After=network.target
@@ -135,22 +212,45 @@ function maybe_install_mongodb() {
 # the set to install.
 function install_conda() {
   local -r the_script="${PANDIR}/tmp/miniconda.sh"
+  local -r the_destination="${PANDIR}/miniconda"
+  if [[ -d "${the_destination}" ]] ; then
+    echo_bar
+    echo
+    echo "Removing previous miniconda installation from ${the_destination}"
+    rm -rf "${the_destination}"
+  fi
   echo_bar
   echo
   echo "Installing miniconda. License at: https://conda.io/docs/license.html"
   wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
        -O "${the_script}"
-  bash "${the_script}" -b -p "${PANDIR}/miniconda"
+  bash "${the_script}" -b -p "${the_destination}"
   rm "${the_script}"
-  add_to_PATH miniconda/bin
+
+  # As per the Anaconda 4.4 release notes, one is supposed to add the following
+  # to .bash_profile, .bashrc or whereever is appropriate:
+  #    . $CONDA_LOCATION/etc/profile.d/conda.sh
+  #    conda activate base
+  # Where CONDA_LOCATION is where Anaconda or miniconda was installed.
+  # We do the first step here, but obviously only we we are actually
+  # installing conda. The second step will be done unconditionally
+  # elsewhere in this file.
+
+  . ${the_destination}/etc/profile.d/conda.sh
+  add_to_profile_before_bashrc \
+      ". ${the_destination}/etc/profile.d/conda.sh"
 }
 
 function install_conda_if_missing() {
   # Intall latest version of Miniconda (Anaconda with
   # fewer packages; any that are needed can then be installed).
-  CONDA_BIN="$(which conda)"  # Assuming is a python3 version if found.
-  if [[ -z "${CONDA_BIN}" ]] ; then
+  # Note that if conda is found, we assume that a Python 3 version is installed.
+  if [[ -z "$(which conda)" ]] ; then
     install_conda
+  else
+    echo_bar
+    echo
+    echo "Reusing existing conda:" "$(which conda)"
   fi
 }
 
@@ -369,48 +469,86 @@ if [[ "${DO_CONDA}" -eq 1 ]] ; then
   install_conda_if_missing
 fi
 
+# Add the astropy channel, i.e. an additional repository in which to
+# look for packages. With conda 4.1.0 and later, by default the highest
+# priority repository that contains a package is used as the source for
+# that package, even if there is a newer version in a lower priority
+# package. And by default the most recently added repository is treated
+# as the highest priority repository. Here we use prepend to be clear
+# that we want astropy to be highest priority.
+if [[ -n "$(conda config --show channels | fgrep astropy)" ]] ; then
+  conda config --remove channels astropy
+fi
+conda config --prepend channels astropy
+
+# And put conda-forge at the back of the line.
+if [[ -n "$(conda config --show channels | fgrep conda-forge)" ]] ; then
+  conda config --remove channels conda-forge
+fi
+conda config --append channels conda-forge
+
+# Use the base Anaconda environment until we're ready to
+# work with the PANOPTES environment.
+conda activate base
 
 # Make sure we use the correct Anaconda environment.
 DO_CREATE_CONDA_ENV=0
-if [[ -z "$(conda info --envs | grep panoptes-env)" ]] ; then
+if [[ -z "$(conda env list | grep panoptes-env)" ]] ; then
   DO_CREATE_CONDA_ENV=1
 elif [[ "${DO_REBUILD_CONDA_ENV}" -eq 1 ]] ; then
-  source activate root
+  echo_bar
+  echo 
+  echo "Removing previous PANOPTES conda env"
   conda remove --all --yes --quiet -n panoptes-env
   DO_CREATE_CONDA_ENV=1
 fi
+
+if [[ "${DO_CONDA}" -eq 1 || "${DO_CREATE_CONDA_ENV}" -eq 1 || \
+      "${DO_PIP_REQUIREMENTS}" -eq 1 ]] ; then
+  echo_bar
+  echo
+  echo "Updating base conda installation."
+  conda update --quiet --yes -n base conda
+fi
+
 if [[ "${DO_CREATE_CONDA_ENV}" -eq 1 ]] ; then
+  echo_bar
+  echo 
+  echo "Creating conda env for PANOPTES: panoptes-env"
   conda create --yes -n panoptes-env python=3
 fi
 
-add_to_profile "source activate panoptes-env"
-source activate panoptes-env
+add_to_profile_before_bashrc "conda activate panoptes-env"
+conda activate panoptes-env
 
 if [[ "${DO_CONDA}" -eq 1 || "${DO_CREATE_CONDA_ENV}" -eq 1 || \
       "${DO_PIP_REQUIREMENTS}" -eq 1 ]] ; then
   echo_bar
   echo
-  echo "Updating conda installation."
-  conda update --quiet --all --yes
+  echo "Updating packages in panoptes-env."
+  conda update -n panoptes-env --quiet --yes conda
+  conda update -n panoptes-env --quiet --yes --all
 fi
 
-
 if [[ "${DO_INSTALL_CONDA_PACKAGES}" -eq 1 ]] ; then
   echo_bar
   echo
-  echo "Installing conda packages"
+  echo "Installing conda packages needed for PANOPTES"
   conda install --yes "--file=${THIS_DIR}/conda-packages-list.txt"
 fi
 
+echo_bar
+echo "PATH=$PATH"
+echo_bar
+
+exit
 
 if [[ "${DO_PIP_REQUIREMENTS}" -eq 1 ]] ; then
+  echo_bar
+  echo
+  echo "Installing Python packages using pip"
   # Upgrade pip itself before installing other python packages.
   pip install -U pip
-  # TODO(jamessynge): Move this script and needed text files into an install
-  # directory.
-  # TODO(wtgee): Consider whether to inline the needed text files into this
-  # file, and add git clone of the PANOPTES repos, so that the user can do
-  # an install with just about two commands (wget script, then run script).
   pip install -r "${POCS}/requirements.txt"
 fi
 
@@ -437,10 +575,11 @@ set +x
 echo
 echo_bar
 echo_bar
-echo
-echo "Remember to update PATH in your shell before running tests"
-echo "and to run \"source activate panoptes-env\""
-echo
+echo "
+Your ${THE_PROFILE} has been modified. To pickup that change,
+please logout completely, then log back in. Don't just open
+a new terminal window.
+"
 
 exit