From 9ec41dbc785082938fc38cfafef0aa71a3388cdd Mon Sep 17 00:00:00 2001
From: Joe Ringgenberg <jringgenberg@zymergen.com>
Date: Thu, 11 Apr 2019 11:41:27 -0700
Subject: [PATCH 1/7] build script and dockerfiles for python 2.7 based AWS
 Lambda

---
 Dockerfile-build-python27-lambda | 86 ++++++++++++++++++++++++++++++++
 Dockerfile-python27-lambda       | 33 ++++++++++++
 build-python27-lambda.sh         | 49 ++++++++++++++++++
 3 files changed, 168 insertions(+)
 create mode 100644 Dockerfile-build-python27-lambda
 create mode 100644 Dockerfile-python27-lambda
 create mode 100755 build-python27-lambda.sh

diff --git a/Dockerfile-build-python27-lambda b/Dockerfile-build-python27-lambda
new file mode 100644
index 0000000..f93d8e0
--- /dev/null
+++ b/Dockerfile-build-python27-lambda
@@ -0,0 +1,86 @@
+# Dockerfile for building RDKit artifacts.
+# This is a heavyweight image containing all aspects of RDKit plus the build system.
+# It's purpose is to create the RDKit artifacts that will be deployed to lighter weigth images.
+
+
+FROM lambci/lambda:build-python2.7 
+
+# centos currently only comes with boost 1.53 which is no good for RDKit.
+# so as a temp measure we exclude installing the boost packages and instead build from source.
+# We can revert this once updated boost packages are available.
+
+RUN yum install -y --enablerepo=epel --setopt=tsflags=nodocs --setopt=override_install_langs=en_US.utf8\
+#  tk-devel\
+  readline-devel\
+  zlib-devel\
+  bzip2-devel\
+  sqlite-devel\
+  @development\
+  cmake3\
+  python27-devel\
+  python27-numpy\
+  #boost\
+  #boost-python\
+  #boost-devel\
+  eigen3\
+  eigen3-devel\
+  swig\
+  git\
+  yum clean all &&\
+  rm -rf /var/cache/yum
+
+
+# Here we build boost from source.
+# This will be unnecessary once updated boost packages are available.
+WORKDIR /root/boost
+RUN curl -L -o boost.tgz http://sourceforge.net/projects/boost/files/boost/1.56.0/boost_1_56_0.tar.gz &&\
+  tar xfz boost.tgz &&\
+  rm -f boost.tgz &&\
+  cd boost_1_56_0 &&\
+  ./bootstrap.sh --with-libraries=python,serialization &&\
+  ./b2 install
+
+# Tar up the built libraries (which have been installed into /usr/local/lib)
+# as we'll need them for the runtime images.
+# They need to go in /usr/lib64
+WORKDIR /usr/local/lib
+RUN  tar cvfz /root/boost-1.56.0.tgz libboost*so.*
+
+WORKDIR /
+
+# Clone the RDKit repo and do the build
+ARG RDKIT_BRANCH=master
+RUN git clone -b $RDKIT_BRANCH --single-branch https://github.com/rdkit/rdkit.git
+
+# hack to build cartridge packages. can be removed once this code hits the repo
+COPY patch_pgsql_rpm.patch /rdkit
+RUN cd /rdkit && patch -p1 < patch_pgsql_rpm.patch
+
+ENV RDBASE=/rdkit
+ENV JAVA_HOME=/usr/lib/jvm/java
+ENV CLASSPATH=$RDBASE/Code/JavaWrappers/gmwrapper/org.RDKit.jar
+
+RUN mkdir $RDBASE/build
+WORKDIR $RDBASE/build
+
+RUN cmake3 -Wno-dev\
+  -DBOOST_ROOT=/root/boost/boost_1_56_0\
+  -DLIB_SUFFIX=64\
+  -DRDK_INSTALL_INTREE=OFF\
+  -DRDK_BUILD_INCHI_SUPPORT=ON\
+  -DRDK_BUILD_AVALON_SUPPORT=ON\
+  -DRDK_BUILD_PYTHON_WRAPPERS=ON\
+  -DRDK_BUILD_SWIG_WRAPPERS=OFF\
+  -DCMAKE_INSTALL_PREFIX=/usr\
+  ..
+
+RUN nproc=$(getconf _NPROCESSORS_ONLN)\
+  && make -j $(( nproc > 2 ? nproc - 2 : 1 ))\
+#  && make install\
+  && cpack3 -G RPM
+
+ENV CLASSPATH=$RDBASE/Code/JavaWrappers/gmwrapper/org.RDKit.jar
+ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$RDBASE/lib:$RDBASE/Code/JavaWrappers/gmwrapper:/usr/lib/x86_64-linux-gnu
+ENV PYTHONPATH=$PYTHONPATH:$RDBASE
+WORKDIR $RDBASE
+
diff --git a/Dockerfile-python27-lambda b/Dockerfile-python27-lambda
new file mode 100644
index 0000000..0dc1ef5
--- /dev/null
+++ b/Dockerfile-python27-lambda
@@ -0,0 +1,33 @@
+# Dockerfile for Python based RDKit implementation
+# Based on Centos7
+# See comments in build-centos.sh for details.
+
+FROM lambci/lambda:build-python2.7 
+
+run yum install -y --setopt=tsflags=nodocs --setopt=override_install_langs=en_US.utf8\
+ python27-numpy\
+ sqlite\
+ sqlite-devel\
+ yum clean -y all &&\
+ rm -rf /var/cache/yum
+
+ARG DOCKER_TAG=Release_2019_03_1
+
+COPY artifacts/lambda/$DOCKER_TAG/rpms/RDKit-*-Linux-Runtime.rpm artifacts/lambda/$DOCKER_TAG/rpms/RDKit-*-Linux-Python.rpm artifacts/lambda/$DOCKER_TAG/boost/boost-1.56.0.tgz /tmp/
+RUN cd /usr/lib64 && tar xvfz /tmp/boost-1.56.0.tgz && rm /tmp/boost-1.56.0.tgz && ls -l /usr/lib64/*boost*
+RUN rpm --nodeps -iv /tmp/*.rpm && rm -f /tmp/*.rpm
+
+RUN mkdir -p /tmp/layer/lib && mkdir -p /tmp/layer/python
+RUN cp -av /usr/lib64/python2.7/dist-packages/rdkit /tmp/layer/python
+RUN cp -av /usr/lib64/libRDKit* /tmp/layer/lib
+RUN cp -av /usr/lib64/libboost_* /tmp/layer/lib
+RUN cp -av /usr/lib64/libsqlite3* /tmp/layer/lib
+
+WORKDIR /tmp/layer
+RUN zip --symlinks -rv rdkit-python27.zip *
+
+WORKDIR /
+
+# add the rdkit user
+RUN useradd -u 1000 -U -G 0 rdkit
+USER 1000
diff --git a/build-python27-lambda.sh b/build-python27-lambda.sh
new file mode 100755
index 0000000..ec9f242
--- /dev/null
+++ b/build-python27-lambda.sh
@@ -0,0 +1,49 @@
+#!/bin/bash
+# 
+# centos based build
+#
+# NOTE - this is a bit a a hack as Centos7 comes with boost version 1.53, and several
+# of the required libraries require this version, but recent RDKit builds (since the 
+# switch to modern C++) require boost 1.56 or later.
+# The solution is to build boost binaries for 1.56 so that RDKit can be built against
+# those and to copy those binaries into the destination image, and to use the --nodeps
+# option when rpm installing the RDKit RPMs.
+# The resulting image has both versions of boost in /usr/lib64 and RDKit seems to be
+# quite happy with this.
+#
+# Credit to Paolo Tosco for helping to work out a strategy for this. 
+#
+# Currently Java and Cartridge images are not built to limit the complexity. Use the
+# debain based images if you need these.
+
+
+set -ex
+
+source params.sh
+
+# build RDKit
+docker build --no-cache -f Dockerfile-build-python27-lambda\
+  -t $BASE/rdkit-build-python27-lambda:$DOCKER_TAG\
+  --build-arg RDKIT_BRANCH=$GIT_BRANCH .
+
+# copy the packages
+rm -rf artifacts/python27-lambda/$DOCKER_TAG
+mkdir -p artifacts/python27-lambda/$DOCKER_TAG/rpms
+mkdir -p artifacts/python27-lambda/$DOCKER_TAG/java
+mkdir -p artifacts/python27-lambda/$DOCKER_TAG/boost
+mkdir -p artifacts/python27-lambda/$DOCKER_TAG/layer
+docker run -it --rm -u $(id -u)\
+  -v $PWD/artifacts/python27-lambda/$DOCKER_TAG:/tohere:Z\
+  $BASE/rdkit-build-python27-lambda:$DOCKER_TAG bash -c 'cp build/*.rpm /tohere/rpms && cp /root/boost-1.56.0.tgz /tohere/boost'
+
+# build image for python
+docker build --no-cache -f Dockerfile-python27-lambda\
+  -t $BASE/rdkit-python27-lambda:$DOCKER_TAG\
+  --build-arg TAG=$DOCKER_TAG .
+echo "Built image informaticsmatters/rdkit-python27-lambda:$DOCKER_TAG"
+
+# copy the assembled layer
+docker run -it --rm -u $(id -u)\
+  -v $PWD/artifacts/python27-lambda/$DOCKER_TAG:/tohere:Z\
+  $BASE/rdkit-python27-lambda:$DOCKER_TAG bash -c 'cp /tmp/layer/rdkit-python27.zip /tohere/layer'
+

From 39f61238e5abf84e9424f6f3abdefb033024caa7 Mon Sep 17 00:00:00 2001
From: Joe Ringgenberg <jringgenberg@zymergen.com>
Date: Fri, 12 Apr 2019 13:25:25 -0700
Subject: [PATCH 2/7] build script and dockerfiles for python 3.6 based AWS
 Lambda

---
 Dockerfile-build-python36-lambda | 92 ++++++++++++++++++++++++++++++++
 Dockerfile-python36-lambda       | 38 +++++++++++++
 build-python36-lambda.sh         | 49 +++++++++++++++++
 3 files changed, 179 insertions(+)
 create mode 100644 Dockerfile-build-python36-lambda
 create mode 100644 Dockerfile-python36-lambda
 create mode 100755 build-python36-lambda.sh

diff --git a/Dockerfile-build-python36-lambda b/Dockerfile-build-python36-lambda
new file mode 100644
index 0000000..e22907e
--- /dev/null
+++ b/Dockerfile-build-python36-lambda
@@ -0,0 +1,92 @@
+# Dockerfile for building RDKit artifacts.
+# This is a heavyweight image containing all aspects of RDKit plus the build system.
+# It's purpose is to create the RDKit artifacts that will be deployed to lighter weigth images.
+
+
+FROM lambci/lambda:build-python3.6 
+
+# centos currently only comes with boost 1.53 which is no good for RDKit.
+# so as a temp measure we exclude installing the boost packages and instead build from source.
+# We can revert this once updated boost packages are available.
+
+RUN yum install -y --enablerepo=epel --setopt=tsflags=nodocs --setopt=override_install_langs=en_US.utf8\
+#  tk-devel\
+  readline-devel\
+  zlib-devel\
+  bzip2-devel\
+  sqlite-devel\
+  @development\
+  cmake3\
+  #boost\
+  #boost-python\
+  #boost-devel\
+  eigen3\
+  eigen3-devel\
+  swig\
+  git\
+  yum clean all &&\
+  rm -rf /var/cache/yum
+
+RUN ln -sf /var/lang/bin/python3.6 /usr/bin/python
+RUN ln -sf /var/lang/bin/python3.6 /usr/bin/python3
+RUN ln -s /var/lang/include/python3.6m /var/lang/include/python3.6
+
+RUN pip install numpy
+
+# Here we build boost from source.
+# This will be unnecessary once updated boost packages are available.
+WORKDIR /root/boost
+RUN curl -L -o boost.tgz http://sourceforge.net/projects/boost/files/boost/1.56.0/boost_1_56_0.tar.gz &&\
+  tar xfz boost.tgz &&\
+  rm -f boost.tgz &&\
+  cd boost_1_56_0 &&\
+  ./bootstrap.sh --with-libraries=python,serialization &&\
+  ./b2 install
+
+# Tar up the built libraries (which have been installed into /usr/local/lib)
+# as we'll need them for the runtime images.
+# They need to go in /usr/lib64
+WORKDIR /usr/local/lib
+RUN  tar cvfz /root/boost-1.56.0.tgz libboost*so.*
+
+WORKDIR /
+
+# Clone the RDKit repo and do the build
+ARG RDKIT_BRANCH=master
+RUN git clone -b $RDKIT_BRANCH --single-branch https://github.com/rdkit/rdkit.git
+
+# hack to build cartridge packages. can be removed once this code hits the repo
+COPY patch_pgsql_rpm.patch /rdkit
+RUN cd /rdkit && patch -p1 < patch_pgsql_rpm.patch
+
+ENV RDBASE=/rdkit
+ENV JAVA_HOME=/usr/lib/jvm/java
+ENV CLASSPATH=$RDBASE/Code/JavaWrappers/gmwrapper/org.RDKit.jar
+
+RUN mkdir $RDBASE/build
+WORKDIR $RDBASE/build
+
+RUN cmake3 -Wno-dev\
+  -DPYTHON_EXECUTABLE=/var/lang/bin/python3.6\
+  -DPYTHON_INCLUDE_DIR=/var/lang/include/python3.6\
+  -DPYTHON_LIBRARY=/var/lang/lib/python3.6/config-3.6m-x86_64-linux-gnu/libpython3.6m.a\
+  -DBOOST_ROOT=/root/boost/boost_1_56_0\
+  -DLIB_SUFFIX=64\
+  -DRDK_INSTALL_INTREE=OFF\
+  -DRDK_BUILD_INCHI_SUPPORT=ON\
+  -DRDK_BUILD_AVALON_SUPPORT=ON\
+  -DRDK_BUILD_PYTHON_WRAPPERS=ON\
+  -DRDK_BUILD_SWIG_WRAPPERS=OFF\
+  -DCMAKE_INSTALL_PREFIX=/usr\
+  ..
+
+RUN nproc=$(getconf _NPROCESSORS_ONLN)\
+  && make -j $(( nproc > 2 ? nproc - 2 : 1 ))\
+#  && make install\
+  && cpack3 -G RPM
+
+ENV CLASSPATH=$RDBASE/Code/JavaWrappers/gmwrapper/org.RDKit.jar
+ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$RDBASE/lib:$RDBASE/Code/JavaWrappers/gmwrapper:/usr/lib/x86_64-linux-gnu
+ENV PYTHONPATH=$PYTHONPATH:$RDBASE
+WORKDIR $RDBASE
+
diff --git a/Dockerfile-python36-lambda b/Dockerfile-python36-lambda
new file mode 100644
index 0000000..cfa6d0a
--- /dev/null
+++ b/Dockerfile-python36-lambda
@@ -0,0 +1,38 @@
+# Dockerfile for Python based RDKit implementation
+# Based on Centos7
+# See comments in build-centos.sh for details.
+
+FROM lambci/lambda:build-python3.6 
+
+RUN yum install -y --setopt=tsflags=nodocs --setopt=override_install_langs=en_US.utf8\
+ sqlite\
+ sqlite-devel\
+ yum clean -y all &&\
+ rm -rf /var/cache/yum
+
+RUN pip install numpy
+RUN ln -s /usr/lib/python3.6/site-packages/rdkit /var/lang/lib/python3.6/site-packages/rdkit
+
+ARG DOCKER_TAG=Release_2019_03_1
+
+COPY artifacts/python36-lambda/$DOCKER_TAG/rpms/RDKit-*-Linux-Runtime.rpm artifacts/python36-lambda/$DOCKER_TAG/rpms/RDKit-*-Linux-Python.rpm artifacts/python36-lambda/$DOCKER_TAG/boost/boost-1.56.0.tgz /tmp/
+RUN cd /usr/lib64 && tar xvfz /tmp/boost-1.56.0.tgz && rm /tmp/boost-1.56.0.tgz && ls -l /usr/lib64/*boost*
+RUN rpm --nodeps -iv /tmp/*.rpm && rm -f /tmp/*.rpm
+
+# create a folder and copy all files for the lambda layer
+RUN mkdir -p /tmp/layer/lib && mkdir -p /tmp/layer/python
+RUN cp -av /usr/lib/python3.6/site-packages/rdkit /tmp/layer/python
+RUN cp -av /var/lang/lib/python3.6/site-packages/numpy /tmp/layer/python
+RUN cp -av /usr/lib64/libRDKit* /tmp/layer/lib
+RUN cp -av /usr/lib64/libboost_* /tmp/layer/lib
+RUN cp -av /usr/lib64/libsqlite3* /tmp/layer/lib
+
+# assemble the lambda layer as a zipfile
+WORKDIR /tmp/layer
+RUN zip --symlinks -rv rdkit-python36.zip *
+
+WORKDIR /
+
+# add the rdkit user
+RUN useradd -u 1000 -U -G 0 rdkit
+USER 1000
diff --git a/build-python36-lambda.sh b/build-python36-lambda.sh
new file mode 100755
index 0000000..95d551a
--- /dev/null
+++ b/build-python36-lambda.sh
@@ -0,0 +1,49 @@
+#!/bin/bash
+# 
+# centos based build
+#
+# NOTE - this is a bit a a hack as Centos7 comes with boost version 1.53, and several
+# of the required libraries require this version, but recent RDKit builds (since the 
+# switch to modern C++) require boost 1.56 or later.
+# The solution is to build boost binaries for 1.56 so that RDKit can be built against
+# those and to copy those binaries into the destination image, and to use the --nodeps
+# option when rpm installing the RDKit RPMs.
+# The resulting image has both versions of boost in /usr/lib64 and RDKit seems to be
+# quite happy with this.
+#
+# Credit to Paolo Tosco for helping to work out a strategy for this. 
+#
+# Currently Java and Cartridge images are not built to limit the complexity. Use the
+# debain based images if you need these.
+
+
+set -ex
+
+source params.sh
+
+# build RDKit
+docker build --no-cache -f Dockerfile-build-python36-lambda\
+  -t $BASE/rdkit-build-python36-lambda:$DOCKER_TAG\
+  --build-arg RDKIT_BRANCH=$GIT_BRANCH .
+
+# copy the packages
+rm -rf artifacts/python36-lambda/$DOCKER_TAG
+mkdir -p artifacts/python36-lambda/$DOCKER_TAG/rpms
+mkdir -p artifacts/python36-lambda/$DOCKER_TAG/java
+mkdir -p artifacts/python36-lambda/$DOCKER_TAG/boost
+mkdir -p artifacts/python36-lambda/$DOCKER_TAG/layer
+docker run -it --rm -u $(id -u)\
+  -v $PWD/artifacts/python36-lambda/$DOCKER_TAG:/tohere:Z\
+  $BASE/rdkit-build-python36-lambda:$DOCKER_TAG bash -c 'cp build/*.rpm /tohere/rpms && cp /root/boost-1.56.0.tgz /tohere/boost'
+
+# build image for python
+docker build --no-cache -f Dockerfile-python36-lambda\
+  -t $BASE/rdkit-python36-lambda:$DOCKER_TAG\
+  --build-arg TAG=$DOCKER_TAG .
+echo "Built image informaticsmatters/rdkit-python36-lambda:$DOCKER_TAG"
+
+# copy the assembled layer
+docker run -it --rm -u $(id -u)\
+  -v $PWD/artifacts/python36-lambda/$DOCKER_TAG:/tohere:Z\
+  $BASE/rdkit-python36-lambda:$DOCKER_TAG bash -c 'cp /tmp/layer/rdkit-python36.zip /tohere/layer'
+

From dbff72485cb33511c6347d5692d30febdf498fbe Mon Sep 17 00:00:00 2001
From: Joe Ringgenberg <jringgenberg@zymergen.com>
Date: Mon, 6 May 2019 12:19:30 -0700
Subject: [PATCH 3/7] cleanup and comments

---
 Dockerfile-build-python27-lambda | 12 ++++++------
 Dockerfile-build-python36-lambda | 18 ++++++++++++------
 Dockerfile-python27-lambda       | 17 +++++++++++------
 Dockerfile-python36-lambda       | 15 +++++++++------
 build-python27-lambda.sh         |  2 +-
 build-python36-lambda.sh         |  2 +-
 6 files changed, 40 insertions(+), 26 deletions(-)

diff --git a/Dockerfile-build-python27-lambda b/Dockerfile-build-python27-lambda
index f93d8e0..57fb077 100644
--- a/Dockerfile-build-python27-lambda
+++ b/Dockerfile-build-python27-lambda
@@ -1,16 +1,16 @@
 # Dockerfile for building RDKit artifacts.
-# This is a heavyweight image containing all aspects of RDKit plus the build system.
-# It's purpose is to create the RDKit artifacts that will be deployed to lighter weigth images.
-
+# This image contains all aspects of RDKit plus the build system.
+# Its purpose is to create the RDKit artifacts that will be deployed to AWS Lambda.
 
+# The LambCI project provides a number of Docker images that closely mimic the
+# AWS Lambda environment.  More details here: https://github.com/lambci/docker-lambda
 FROM lambci/lambda:build-python2.7 
 
-# centos currently only comes with boost 1.53 which is no good for RDKit.
-# so as a temp measure we exclude installing the boost packages and instead build from source.
+# AWS Lambda is based on CentOS, which only provides Boost 1.53 and does not work with RDKit.
+# For the time being, exclude installing the boost packages and instead build from source.
 # We can revert this once updated boost packages are available.
 
 RUN yum install -y --enablerepo=epel --setopt=tsflags=nodocs --setopt=override_install_langs=en_US.utf8\
-#  tk-devel\
   readline-devel\
   zlib-devel\
   bzip2-devel\
diff --git a/Dockerfile-build-python36-lambda b/Dockerfile-build-python36-lambda
index e22907e..c60c4e7 100644
--- a/Dockerfile-build-python36-lambda
+++ b/Dockerfile-build-python36-lambda
@@ -1,16 +1,16 @@
 # Dockerfile for building RDKit artifacts.
-# This is a heavyweight image containing all aspects of RDKit plus the build system.
-# It's purpose is to create the RDKit artifacts that will be deployed to lighter weigth images.
-
+# This image contains all aspects of RDKit plus the build system.
+# Its purpose is to create the RDKit artifacts that will be deployed to AWS Lambda.
 
+# The LambCI project provides a number of Docker images that closely mimic the
+# AWS Lambda environment.  More details here: https://github.com/lambci/docker-lambda
 FROM lambci/lambda:build-python3.6 
 
-# centos currently only comes with boost 1.53 which is no good for RDKit.
-# so as a temp measure we exclude installing the boost packages and instead build from source.
+# AWS Lambda is based on CentOS, which only provides Boost 1.53 and does not work with RDKit.
+# For the time being, exclude installing the boost packages and instead build from source.
 # We can revert this once updated boost packages are available.
 
 RUN yum install -y --enablerepo=epel --setopt=tsflags=nodocs --setopt=override_install_langs=en_US.utf8\
-#  tk-devel\
   readline-devel\
   zlib-devel\
   bzip2-devel\
@@ -27,10 +27,15 @@ RUN yum install -y --enablerepo=epel --setopt=tsflags=nodocs --setopt=override_i
   yum clean all &&\
   rm -rf /var/cache/yum
 
+# Unlike the 'build-python2.7' image, this LambCI image does not install Python from
+# the Amazon repo and instead builds from source.  The Python base is /var/lang/bin/python3.6,
+# which must be aliased in order for the RDKit build and packaging scripts to locate
+# the interpreter.
 RUN ln -sf /var/lang/bin/python3.6 /usr/bin/python
 RUN ln -sf /var/lang/bin/python3.6 /usr/bin/python3
 RUN ln -s /var/lang/include/python3.6m /var/lang/include/python3.6
 
+# Numpy for Python 3.6 is not available from the Amazon repo.
 RUN pip install numpy
 
 # Here we build boost from source.
@@ -66,6 +71,7 @@ ENV CLASSPATH=$RDBASE/Code/JavaWrappers/gmwrapper/org.RDKit.jar
 RUN mkdir $RDBASE/build
 WORKDIR $RDBASE/build
 
+# Extra options here to let the RDKit build know which Python install to use
 RUN cmake3 -Wno-dev\
   -DPYTHON_EXECUTABLE=/var/lang/bin/python3.6\
   -DPYTHON_INCLUDE_DIR=/var/lang/include/python3.6\
diff --git a/Dockerfile-python27-lambda b/Dockerfile-python27-lambda
index 0dc1ef5..fc0cf73 100644
--- a/Dockerfile-python27-lambda
+++ b/Dockerfile-python27-lambda
@@ -1,28 +1,33 @@
-# Dockerfile for Python based RDKit implementation
-# Based on Centos7
-# See comments in build-centos.sh for details.
+# Dockerfile for packaging a Python based RDKit implementation to deploy
+# as an AWS Lambda layer.  See comments in build-python27-lambda.sh for
+# details.
 
 FROM lambci/lambda:build-python2.7 
 
-run yum install -y --setopt=tsflags=nodocs --setopt=override_install_langs=en_US.utf8\
+RUN yum install -y --setopt=tsflags=nodocs --setopt=override_install_langs=en_US.utf8\
  python27-numpy\
  sqlite\
  sqlite-devel\
  yum clean -y all &&\
  rm -rf /var/cache/yum
 
-ARG DOCKER_TAG=Release_2019_03_1
+ARG DOCKER_TAG=latest
 
-COPY artifacts/lambda/$DOCKER_TAG/rpms/RDKit-*-Linux-Runtime.rpm artifacts/lambda/$DOCKER_TAG/rpms/RDKit-*-Linux-Python.rpm artifacts/lambda/$DOCKER_TAG/boost/boost-1.56.0.tgz /tmp/
+COPY artifacts/python27-lambda/$DOCKER_TAG/rpms/RDKit-*-Linux-Runtime.rpm artifacts/python27-lambda/$DOCKER_TAG/rpms/RDKit-*-Linux-Python.rpm artifacts/python27-lambda/$DOCKER_TAG/boost/boost-1.56.0.tgz /tmp/
 RUN cd /usr/lib64 && tar xvfz /tmp/boost-1.56.0.tgz && rm /tmp/boost-1.56.0.tgz && ls -l /usr/lib64/*boost*
 RUN rpm --nodeps -iv /tmp/*.rpm && rm -f /tmp/*.rpm
 
+# Copy all files for the lambda layer.
+# Note this does NOT include the NumPy dependency - instead this should
+# be provided by using this layer with the AWS provided SciPy1x layer when
+# creating a lambda function.
 RUN mkdir -p /tmp/layer/lib && mkdir -p /tmp/layer/python
 RUN cp -av /usr/lib64/python2.7/dist-packages/rdkit /tmp/layer/python
 RUN cp -av /usr/lib64/libRDKit* /tmp/layer/lib
 RUN cp -av /usr/lib64/libboost_* /tmp/layer/lib
 RUN cp -av /usr/lib64/libsqlite3* /tmp/layer/lib
 
+# Assemble the lambda layer as a zipfile
 WORKDIR /tmp/layer
 RUN zip --symlinks -rv rdkit-python27.zip *
 
diff --git a/Dockerfile-python36-lambda b/Dockerfile-python36-lambda
index cfa6d0a..40bfa85 100644
--- a/Dockerfile-python36-lambda
+++ b/Dockerfile-python36-lambda
@@ -1,6 +1,6 @@
-# Dockerfile for Python based RDKit implementation
-# Based on Centos7
-# See comments in build-centos.sh for details.
+# Dockerfile for packaging a Python based RDKit implementation to deploy
+# as an AWS Lambda layer.  See comments in build-python36-lambda.sh for
+# details.
 
 FROM lambci/lambda:build-python3.6 
 
@@ -13,13 +13,16 @@ RUN yum install -y --setopt=tsflags=nodocs --setopt=override_install_langs=en_US
 RUN pip install numpy
 RUN ln -s /usr/lib/python3.6/site-packages/rdkit /var/lang/lib/python3.6/site-packages/rdkit
 
-ARG DOCKER_TAG=Release_2019_03_1
+ARG DOCKER_TAG=latest
 
 COPY artifacts/python36-lambda/$DOCKER_TAG/rpms/RDKit-*-Linux-Runtime.rpm artifacts/python36-lambda/$DOCKER_TAG/rpms/RDKit-*-Linux-Python.rpm artifacts/python36-lambda/$DOCKER_TAG/boost/boost-1.56.0.tgz /tmp/
 RUN cd /usr/lib64 && tar xvfz /tmp/boost-1.56.0.tgz && rm /tmp/boost-1.56.0.tgz && ls -l /usr/lib64/*boost*
 RUN rpm --nodeps -iv /tmp/*.rpm && rm -f /tmp/*.rpm
 
-# create a folder and copy all files for the lambda layer
+# Copy all files for the lambda layer
+# Note that this DOES include the NumPy dependency - attempts to use
+# the layer built from this image with the AWS provided Python 3.6
+# SciPy1x layer were not successful.
 RUN mkdir -p /tmp/layer/lib && mkdir -p /tmp/layer/python
 RUN cp -av /usr/lib/python3.6/site-packages/rdkit /tmp/layer/python
 RUN cp -av /var/lang/lib/python3.6/site-packages/numpy /tmp/layer/python
@@ -27,7 +30,7 @@ RUN cp -av /usr/lib64/libRDKit* /tmp/layer/lib
 RUN cp -av /usr/lib64/libboost_* /tmp/layer/lib
 RUN cp -av /usr/lib64/libsqlite3* /tmp/layer/lib
 
-# assemble the lambda layer as a zipfile
+# Assemble the lambda layer as a zipfile
 WORKDIR /tmp/layer
 RUN zip --symlinks -rv rdkit-python36.zip *
 
diff --git a/build-python27-lambda.sh b/build-python27-lambda.sh
index ec9f242..d4af186 100755
--- a/build-python27-lambda.sh
+++ b/build-python27-lambda.sh
@@ -39,7 +39,7 @@ docker run -it --rm -u $(id -u)\
 # build image for python
 docker build --no-cache -f Dockerfile-python27-lambda\
   -t $BASE/rdkit-python27-lambda:$DOCKER_TAG\
-  --build-arg TAG=$DOCKER_TAG .
+  --build-arg DOCKER_TAG=$DOCKER_TAG .
 echo "Built image informaticsmatters/rdkit-python27-lambda:$DOCKER_TAG"
 
 # copy the assembled layer
diff --git a/build-python36-lambda.sh b/build-python36-lambda.sh
index 95d551a..9679fd0 100755
--- a/build-python36-lambda.sh
+++ b/build-python36-lambda.sh
@@ -39,7 +39,7 @@ docker run -it --rm -u $(id -u)\
 # build image for python
 docker build --no-cache -f Dockerfile-python36-lambda\
   -t $BASE/rdkit-python36-lambda:$DOCKER_TAG\
-  --build-arg TAG=$DOCKER_TAG .
+  --build-arg DOCKER_TAG=$DOCKER_TAG .
 echo "Built image informaticsmatters/rdkit-python36-lambda:$DOCKER_TAG"
 
 # copy the assembled layer

From 1c6b04113a961c14963d051e0bb64a62c87702cf Mon Sep 17 00:00:00 2001
From: Joe Ringgenberg <jringgenberg@zymergen.com>
Date: Mon, 6 May 2019 14:15:32 -0700
Subject: [PATCH 4/7] builds only work with 2018_09 release

---
 params.sh | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/params.sh b/params.sh
index 210618e..e777969 100644
--- a/params.sh
+++ b/params.sh
@@ -1,7 +1,7 @@
-export DOCKER_TAG=latest
+export DOCKER_TAG=Release_2018_09_3
 export GIT_REPO=https://github.com/rdkit/rdkit.git
-export GIT_BRANCH=master
-unset GIT_TAG
+export GIT_BRANCH=Release_2018_09_3
+export GIT_TAG=$DOCKER_TAG
 
 export BASE=informaticsmatters
-echo "DOCKER_TAG=$DOCKER_TAG GIT_BRANCH=$GIT_BRANCH no tag"
+echo "DOCKER_TAG=$DOCKER_TAG GIT_BRANCH=$GIT_BRANCH GIT_TAG=$GIT_TAG"

From 1cb78aa8d6a80bde8d32289f3546519bcf2dc809 Mon Sep 17 00:00:00 2001
From: Joe Ringgenberg <jringgenberg@zymergen.com>
Date: Wed, 8 May 2019 09:00:42 -0700
Subject: [PATCH 5/7] tweak comments

---
 build-python27-lambda.sh | 6 +-----
 build-python36-lambda.sh | 6 +-----
 2 files changed, 2 insertions(+), 10 deletions(-)

diff --git a/build-python27-lambda.sh b/build-python27-lambda.sh
index d4af186..e402804 100755
--- a/build-python27-lambda.sh
+++ b/build-python27-lambda.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 # 
-# centos based build
+# AWS Lambda based build
 #
 # NOTE - this is a bit a a hack as Centos7 comes with boost version 1.53, and several
 # of the required libraries require this version, but recent RDKit builds (since the 
@@ -12,10 +12,6 @@
 # quite happy with this.
 #
 # Credit to Paolo Tosco for helping to work out a strategy for this. 
-#
-# Currently Java and Cartridge images are not built to limit the complexity. Use the
-# debain based images if you need these.
-
 
 set -ex
 
diff --git a/build-python36-lambda.sh b/build-python36-lambda.sh
index 9679fd0..ffe5703 100755
--- a/build-python36-lambda.sh
+++ b/build-python36-lambda.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 # 
-# centos based build
+# AWS Lambda based build
 #
 # NOTE - this is a bit a a hack as Centos7 comes with boost version 1.53, and several
 # of the required libraries require this version, but recent RDKit builds (since the 
@@ -12,10 +12,6 @@
 # quite happy with this.
 #
 # Credit to Paolo Tosco for helping to work out a strategy for this. 
-#
-# Currently Java and Cartridge images are not built to limit the complexity. Use the
-# debain based images if you need these.
-
 
 set -ex
 

From 2c06e0d189e6773522e6b65030aca2ffa141cde0 Mon Sep 17 00:00:00 2001
From: Joe Ringgenberg <jringgenberg@zymergen.com>
Date: Wed, 8 May 2019 09:02:59 -0700
Subject: [PATCH 6/7] tweak comments

---
 Dockerfile-python27-lambda | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile-python27-lambda b/Dockerfile-python27-lambda
index fc0cf73..4b5d1ec 100644
--- a/Dockerfile-python27-lambda
+++ b/Dockerfile-python27-lambda
@@ -19,7 +19,7 @@ RUN rpm --nodeps -iv /tmp/*.rpm && rm -f /tmp/*.rpm
 
 # Copy all files for the lambda layer.
 # Note this does NOT include the NumPy dependency - instead this should
-# be provided by using this layer with the AWS provided SciPy1x layer when
+# be provided by using this layer together with the public AWS SciPy1x layer when
 # creating a lambda function.
 RUN mkdir -p /tmp/layer/lib && mkdir -p /tmp/layer/python
 RUN cp -av /usr/lib64/python2.7/dist-packages/rdkit /tmp/layer/python

From 7352901a1a4e265c31540be7ce29e24d20a4f098 Mon Sep 17 00:00:00 2001
From: Joe Ringgenberg <jringgenberg@zymergen.com>
Date: Mon, 20 May 2019 13:06:20 -0700
Subject: [PATCH 7/7] code review, don't apply cartridge patch

---
 Dockerfile-build-python27-lambda | 4 ----
 Dockerfile-build-python36-lambda | 4 ----
 2 files changed, 8 deletions(-)

diff --git a/Dockerfile-build-python27-lambda b/Dockerfile-build-python27-lambda
index 57fb077..e5395c7 100644
--- a/Dockerfile-build-python27-lambda
+++ b/Dockerfile-build-python27-lambda
@@ -52,10 +52,6 @@ WORKDIR /
 ARG RDKIT_BRANCH=master
 RUN git clone -b $RDKIT_BRANCH --single-branch https://github.com/rdkit/rdkit.git
 
-# hack to build cartridge packages. can be removed once this code hits the repo
-COPY patch_pgsql_rpm.patch /rdkit
-RUN cd /rdkit && patch -p1 < patch_pgsql_rpm.patch
-
 ENV RDBASE=/rdkit
 ENV JAVA_HOME=/usr/lib/jvm/java
 ENV CLASSPATH=$RDBASE/Code/JavaWrappers/gmwrapper/org.RDKit.jar
diff --git a/Dockerfile-build-python36-lambda b/Dockerfile-build-python36-lambda
index c60c4e7..5ef4ff8 100644
--- a/Dockerfile-build-python36-lambda
+++ b/Dockerfile-build-python36-lambda
@@ -60,10 +60,6 @@ WORKDIR /
 ARG RDKIT_BRANCH=master
 RUN git clone -b $RDKIT_BRANCH --single-branch https://github.com/rdkit/rdkit.git
 
-# hack to build cartridge packages. can be removed once this code hits the repo
-COPY patch_pgsql_rpm.patch /rdkit
-RUN cd /rdkit && patch -p1 < patch_pgsql_rpm.patch
-
 ENV RDBASE=/rdkit
 ENV JAVA_HOME=/usr/lib/jvm/java
 ENV CLASSPATH=$RDBASE/Code/JavaWrappers/gmwrapper/org.RDKit.jar