Merge pull request #172 from SystemsGenetics/docker-update

Docker update

docker/Dockerfile

@@ -4,6 +4,7 @@ MAINTAINER Ben Shealy <btsheal@clemson.edu>
 ARG NVIDIA_HEADLESS=0
 ARG ACE_REVISION="develop"
 ARG KINC_REVISION="develop"
+ARG KINC_R_REVISION="master"
 
 ENV CUDADIR="/usr/local/cuda"
 ENV CPLUS_INCLUDE_PATH="${CUDADIR}/include:${CPLUS_INCLUDE_PATH}"
@@ -24,7 +25,8 @@ RUN apt-get update -qq \
 		ocl-icd-opencl-dev \
 		python3-pip
 
-# install headless driver for cpu image
+
+# Install headless driver for cpu image
 RUN if [ ${NVIDIA_HEADLESS} = 1 ]; then apt-get install -qq -y nvidia-headless-418 ; fi
 
 # add NVIDIA platform to OpenCL
@@ -43,11 +45,10 @@ RUN git clone -q https://github.com/kthohr/stats \
 # install ACE
 WORKDIR /opt
 
-ADD https://api.github.com/repos/SystemsGenetics/ACE/git/refs/heads/${ACE_REVISION} ace-version.json
 RUN git clone -q https://github.com/SystemsGenetics/ACE.git \
 	&& cd ACE/build \
 	&& git checkout -q ${ACE_REVISION} \
-	&& qmake ../src/ACE.pro GUI=no \
+	&& qmake ../src/ACE.pro \
 	&& make -s -j $(nproc) \
 	&& make -s qmake_all \
 	&& make -s install
@@ -57,20 +58,69 @@ ENV LD_LIBRARY_PATH "/usr/local/lib:$LD_LIBRARY_PATH"
 # install KINC
 WORKDIR /opt
 
-ADD https://api.github.com/repos/SystemsGenetics/KINC/git/refs/heads/${KINC_REVISION} kinc-version.json
-RUN git clone -q https://github.com/SystemsGenetics/KINC.git \
-	&& mkdir -p KINC/build \
-	&& cd KINC/build \
+# For older version of KINC we need to use qmake. For newer versions after 3.3.x we
+# can use the make file in the root directory of KINC.
+RUN if echo "${KINC_REVISION}" | grep -Eq 'v3\.[32]\.[0-9]$' ; then \
+    git clone -q https://github.com/SystemsGenetics/KINC.git \
+    && cd KINC \
 	&& git checkout -q ${KINC_REVISION} \
-	&& qmake ../src/KINC.pro GUI=no \
+    && cd build \
+	&& qmake ../src/KINC.pro \
 	&& make -s -j $(nproc) \
 	&& make -s qmake_all \
-	&& make -s install
+	&& make -s install; \
+else \
+    git clone -q https://github.com/SystemsGenetics/KINC.git \
+    && cd KINC \
+	&& git checkout -q ${KINC_REVISION} \
+	&& make -s -j $(nproc) \
+	&& make -s install; \
+fi
+
+
+# Add in a few additional requirements for the >=3.4 version of KINC. These are needed
+# for the R and Python scripts in the bin folder.
+RUN if ! echo "${KINC_REVISION}" | grep -Eq 'v3\.[32]\.[0-9]$' ; then \
+    apt-get install -qq -y \
+        m4 \
+        autoconf \
+        automake \
+        libxml2-dev \
+        bison \
+        flex \
+        build-essential \
+        libcurl4-gnutls-dev \
+        libssl-dev \
+        software-properties-common; \
+fi
+
+# Install KINC.R
+ENV DEBIAN_FRONTEND=noninteractive
+RUN if ! echo "${KINC_REVISION}" | grep -Eq 'v3\.[32]\.[0-9]$' ; then \
+    apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 \
+    && add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/' \
+    && apt-get update -qq \
+    && apt-get -qq install -y r-base \
+    && R -q -e "install.packages('devtools', dependencies=TRUE, repos='http://cran.us.r-project.org')" \
+    && R -e "library('devtools'); install_github('SystemsGenetics/KINC.R', ref='${KINC_R_REVISION}')"; \
+fi
 
 # install python dependencies
 WORKDIR /opt/KINC
 
-RUN pip3 install -q -r requirements.txt
+RUN if [ -e requirements.txt ]; then pip3 install  -r requirements.txt; fi
+
+
 
 # initialize default work directory
 WORKDIR /workspace
+
+# Tini for signal processing and zombie killing.
+ENV TINI_VERSION v0.19.0
+ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /tini
+RUN chmod +x /tini
+
+
+# Define the command and parameters that will be executed when this
+# container is first run.
+ENTRYPOINT ["/tini", "--"]

docker/Makefile

@@ -1,40 +1,77 @@
-all: latest v3.4.x v3.3.x v3.2.x
+all: develop latest v3.4.x v3.3.x v3.2.x
 
-latest:
+develop: develop-cpu develop-gpu
+
+develop-cpu:
+	docker build \
+            -t systemsgenetics/kinc:develop-cpu \
+            --build-arg NVIDIA_HEADLESS=1 \
+            --build-arg ACE_REVISION=v3.2.0 \
+            --build-arg KINC_REVISION=develop \
+            --build-arg KINC_R_REVISION=v1.2 \
+            .
+
+develop-gpu:
+    docker build \
+            -t systemsgenetics/kinc:develop-gpu \
+            --build-arg NVIDIA_HEADLESS=0 \
+            --build-arg ACE_REVISION=v3.2.0 \
+            --build-arg KINC_REVISION=develop \
+            --build-arg KINC_R_REVISION=v1.2 \
+            .
+
+
+latest: latest-cpu latest-gpu
+
+latest-cpu:
 	docker build \
 		-t systemsgenetics/kinc:latest-cpu \
 		--build-arg NVIDIA_HEADLESS=1 \
-		--build-arg ACE_REVISION=develop \
-		--build-arg KINC_REVISION=develop \
+		--build-arg ACE_REVISION=v3.2.0 \
+		--build-arg KINC_REVISION=v3.4.2 \
+		--build-arg KINC_R_REVISION=v1.2 \
 		.
+
+latest-gpu:
 	docker build \
 		-t systemsgenetics/kinc:latest-gpu \
 		--build-arg NVIDIA_HEADLESS=0 \
-		--build-arg ACE_REVISION=develop \
-		--build-arg KINC_REVISION=develop \
+		--build-arg ACE_REVISION=v3.2.0 \
+		--build-arg KINC_REVISION=v3.4.2 \
+		--build-arg KINC_R_REVISION=v1.2 \
 		.
 
-v3.4.x:
+v3.4.x: v3.4.x-cpu v3.4.x-gpu
+
+v3.4.x-cpu:
 	docker build \
 		-t systemsgenetics/kinc:3.4.2-cpu \
 		--build-arg NVIDIA_HEADLESS=1 \
 		--build-arg ACE_REVISION=v3.2.0 \
 		--build-arg KINC_REVISION=v3.4.2 \
+		--build-arg KINC_R_REVISION=v1.2 \
 		.
+
+v3.4.x-gpu:
 	docker build \
 		-t systemsgenetics/kinc:3.4.2-gpu \
 		--build-arg NVIDIA_HEADLESS=0 \
 		--build-arg ACE_REVISION=v3.2.0 \
 		--build-arg KINC_REVISION=v3.4.2 \
+		--build-arg KINC_R_REVISION=v1.2 \
 		.
 
-v3.3.x:
+v3.3.x: v3.3.x-cpu v3.3.x-gpu
+
+v3.3.x-cpu:
 	docker build \
 		-t systemsgenetics/kinc:3.3.0-cpu \
 		--build-arg NVIDIA_HEADLESS=1 \
 		--build-arg ACE_REVISION=v3.1.0 \
 		--build-arg KINC_REVISION=v3.3.0 \
 		.
+
+v3.3.x-gpu:
 	docker build \
 		-t systemsgenetics/kinc:3.3.0-gpu \
 		--build-arg NVIDIA_HEADLESS=0 \
@@ -45,12 +82,14 @@ v3.3.x:
 v3.2.x:
 	docker build \
 		-t systemsgenetics/kinc:3.2.2 \
-		--build-arg NVIDIA_HEADLESS=0 \
+		--build-arg NVIDIA_HEADLESS=1 \
 		--build-arg ACE_REVISION=v3.0.2 \
 		--build-arg KINC_REVISION=v3.2.2 \
 		.
 
 push:
+	docker push systemsgenetics/kinc:develop-cpu
+	docker push systemsgenetics/kinc:develop-gpu
 	docker push systemsgenetics/kinc:latest-cpu
 	docker push systemsgenetics/kinc:latest-gpu
 	docker push systemsgenetics/kinc:3.4.2-cpu
@@ -60,6 +99,8 @@ push:
 	docker push systemsgenetics/kinc:3.2.2
 
 pull:
+	docker pull systemsgenetics/kinc:develop-cpu
+	docker pull systemsgenetics/kinc:develop-gpu
 	docker pull systemsgenetics/kinc:latest-cpu
 	docker pull systemsgenetics/kinc:latest-gpu
 	docker pull systemsgenetics/kinc:3.4.2-cpu
@@ -69,6 +110,8 @@ pull:
 	docker pull systemsgenetics/kinc:3.2.2
 
 clean:
+	docker image rm -f systemsgenetics/kinc:develop-cpu
+	docker image rm -f systemsgenetics/kinc:develop-gpu
 	docker image rm -f systemsgenetics/kinc:latest-cpu
 	docker image rm -f systemsgenetics/kinc:latest-gpu
 	docker image rm -f systemsgenetics/kinc:3.4.2-cpu

docs/usage.rst

@@ -518,25 +518,82 @@ This solution does require installation of `Docker <https://www.docker.com/>`_ w
 
 The KINC docker image comes pre-installed with all dependencies. The Dockerfile for KINC is available in the KINC Github repository, and Docker images are maintained on DockerHub under ``systemsgenetics/kinc``. This method currently does not support the GUI version of KINC.
 
-To use KINC in an interactive Docker container execute the following:
+Interactive Mode
+````````````````
+To use KINC in an interactive Docker container **with GPUs** execute the following:
+
 
 .. code:: bash
 
-  nvidia-docker run --rm -it systemsgenetics/kinc:3.4.2 bash
+  docker run --gpus all --rm -it --net=host -v ${PWD}:/workspace -u $(id -u ${USER})  systemsgenetics/kinc:3.4.2-gpu /bin/bash
+
+The command above will provide access to the terminal inside of the `systemsgenetics/kinc:3.4.2-gpu` image.
+
+To use KINC in an interactive Docker container **without GPUs** execute the following:
+
+.. code:: bash
+
+  docker run --gpus all --rm -it --net=host -v ${PWD}:/workspace -u $(id -u ${USER})  systemsgenetics/kinc:3.4.2-cpu /bin/bash
+
+The above command uses the image `systemsgenetics/kinc:3.4.2-cpu` (note the "-cpu" suffix).
 
-The command above will provide access to the terminal inside of the image where commands such as the following can be executed:
+The following describes the meaning of each argument in the commands above:
+
+- `--gpus all`:  ensures that the NVidia CUDA libraries are present in the image. This is needed even if using only CPUs.
+- `--rm`:  will cause the container to be cleaned up after you exit.
+- `--it`:  tells Docker to run in interactive mode with a terminal
+- `--net=host`:  exposes network ports in the image to your local machine. This is needed to use the Docker image for the 3D KINC viewer.
+- `-v ${PWD}:/workspace`: adds the current directory on the local machine as a filesystem in the image accessible via `/workspace`.  This allows you to work with files on your local machine inside of the image.
+- `-u $(id -u ${USER})`:  logs you in as your local user account so that any files created within directories mounted by the image are saved with your user account.
+
+Once inside the KINC Docker image you can execute commands such as the following:
 
 .. code:: bash
 
   > nvidia-smi
   > kinc settings
 
-You will need to share the input and output data between the Docker container and the host machine, which can be done by mounting a directory with the ``-v`` argument.  The example below mounts the current directory specified by the `$PWD` environment variable onto the `/root` directory of the image:
+Test The Example Data
+`````````````````````
+
+To test the docker image using the example data that comes with KINC. Run the following inside of the KINC source directory on your local machine:
+
+.. code:: bash
+
+  docker run --gpus all --rm -it --net=host -v ${PWD}:/workspace -u $(id -u ${USER})  systemsgenetics/kinc:3.4.2-cpu /bin/bash
+
+Next run the following commands inside of the container:
 
 .. code:: bash
 
-  nvidia-docker run --rm -it -v $PWD:/root systemsgenetics/kinc:3.4.2 bash
-  > ls
+  cd /workspace/example
+  ./kinc-gmm-run.sh
+
+Using the 3D Visualization Tool
+```````````````````````````````
+To use the 3D visaulization tool to explore a KINC created network first start an interactive session in the directory where the network file(s) are stored:
+
+.. code:: bash
+
+  docker run --gpus all --rm -it --net=host -v ${PWD}:/workspace -u $(id -u ${USER})  systemsgenetics/kinc:3.4.2-cpu /bin/bash
+
+Then  run the `kinc-3d-viewer.py`.  For example, if the example data is already fully processed using the steps in the previous section you can view the results with the viewer with the following commands.
+
+.. code:: bash
+
+  cd /workspace/example/results-kinc-gmm-run
+  kinc-3d-viewer.py \
+    --net "PRJNA301554.slim.GEM.log2.paf-th0.00-p1e-3-rsqr0.30-filtered-th_ranked.csGCN.txt" \
+    --emx "../data/PRJNA301554.slim.GEM.log2.txt" \
+    --amx "../data/PRJNA301554.slim.annotations.txt"
+
+The first time the viewer is run you will see output about creating 2D and 3D layouts. Once completed you will see a line of text similar to the following:
+
+.. code::
+
+    * Running on http://127.0.0.1:8050/ (Press CTRL+C to quit)
+
+Copy the URL into a web browser and view the network.
 
 Automating KINC with Nextflow
 -----------------------------

requirements.txt

@@ -4,3 +4,8 @@ numpy
 pandas
 scipy
 seaborn
+python-igraph
+plotly
+fa2
+dash
+progress