Docker Tags in line with ark-analysis Version (#636)

* docker argument adjustments in .travis.yml

* no pypi upload

* adjust docker part

* adjust docker part

* docker hell

* docker hell2

* docker fix test

* travis fix

* reverted pypi_deploy on tags: False -> on tags: True

* small updates

.travis.yml

@@ -41,11 +41,10 @@ jobs:
       python: 3.7
       script:
         - "travis_wait 120 sleep 7200 &"
-        - echo "$DOCKER_PASSWORD" | docker login -u "$DOCKER_USERNAME" --password-stdin 
-        - docker build -t "$TRAVIS_REPO_SLUG" . 1> /dev/null
-        - docker tag "$TRAVIS_REPO_SLUG" "$TRAVIS_REPO_SLUG":latest
-        - docker tag "$TRAVIS_REPO_SLUG" "$TRAVIS_REPO_SLUG":"${TRAVIS_TAG}"
-        - docker push "$TRAVIS_REPO_SLUG"
+        - echo "$DOCKER_PASSWORD" | docker login -u "$DOCKER_USERNAME" --password-stdin
+        # Tag the image with a version such as vX.Y.Z,
+        - docker build -t "$TRAVIS_REPO_SLUG":"$TRAVIS_TAG" . 1> /dev/null
+        - docker push --all-tags "$TRAVIS_REPO_SLUG"
 
 after_success:
   - coveralls

Dockerfile

@@ -5,6 +5,8 @@ RUN apt-get update
 
 # install dependencies needed for setting up R
 RUN apt-get install -y lsb-release dirmngr gnupg apt-transport-https ca-certificates software-properties-common
+RUN apt-get install -y libharfbuzz-dev libfribidi-dev
+RUN apt-get -y install libcurl4-gnutls-dev
 
 # set up the key for adding the R repo
 RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 95C0FAF38DB3CCAD0C080A7BDC78B2DDEABC47B7
@@ -23,6 +25,17 @@ RUN apt-get install -y cmake
 
 WORKDIR /scripts
 
+# Install R dependency packages
+RUN R -e "install.packages('arrow')"
+RUN R -e "install.packages('data.table')"
+RUN R -e "install.packages('doParallel')"
+RUN R -e "install.packages('foreach')"
+RUN R -e "install.packages('BiocManager')"
+RUN R -e "install.packages('devtools')"
+RUN R -e "library(devtools); devtools::install_github('angelolab/FlowSOM')"
+RUN R -e "BiocManager::install('ConsensusClusterPlus')"
+
+# Install ark-analysis
 # copy over the requirements.txt, install dependencies, and README
 COPY setup.py requirements.txt README.md /opt/ark-analysis/
 RUN pip install -r /opt/ark-analysis/requirements.txt
@@ -33,16 +46,5 @@ COPY ark /opt/ark-analysis/ark
 # Install the package via setup.py
 RUN pip install /opt/ark-analysis
 
-# Install R dependency packages
-RUN R -e "install.packages('arrow')"
-RUN R -e "install.packages('data.table')"
-RUN R -e "install.packages('doParallel')"
-RUN R -e "install.packages('foreach')"
-RUN R -e "install.packages('BiocManager')"
-RUN R -e "BiocManager::install('FlowSOM')"
-RUN R -e "install.packages('devtools')"
-RUN R -e "library(devtools); devtools::install_github('angelolab/FlowSOM')" # overwrite base FlowSOM with forked FlowSOM
-RUN R -e "BiocManager::install('ConsensusClusterPlus')"
-
 # jupyter lab
 CMD jupyter lab --ip=0.0.0.0 --allow-root --no-browser --port=$JUPYTER_PORT --notebook-dir=/$JUPYTER_DIR