Merge pull request #110 from obophenotype/anitacaron/issue108

Containerise CCF_tools dependencies

Author: Anita Caron

.github/workflows/build.yaml

@@ -17,7 +17,7 @@ jobs:
   build:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.2.23
+    container: anitacaron/ccf-tools-dep
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
@@ -30,4 +30,4 @@ jobs:
       - name: verify and build
         env:
           DEFAULT_BRANCH: master
-        run: mkdir resources/ASCT-b_tables && cd src && make -f test.mk
+        run: mkdir resources/ASCT-b_tables && cd src && make JOBS='Kidney'

Dockerfile

@@ -0,0 +1,38 @@
+FROM ubuntu:20.04
+LABEL maintainer="anitac@ebi.ac.uk" 
+
+WORKDIR /tools
+
+ENV ROBOT v1.8.1
+ARG ROBOT_JAR=https://github.com/ontodev/robot/releases/download/$ROBOT/robot.jar
+ENV ROBOT_JAR ${ROBOT_JAR}
+
+RUN apt-get update && \
+    DEBIAN_FRONTEND="noninteractive" apt-get install -y --no-install-recommends \
+        git \
+        openjdk-11-jre-headless \
+        python3-pip \
+        python-is-python3 \
+        make \
+        unzip \
+        curl \
+        jq \
+        graphviz \
+        nodejs \
+        npm
+
+###### robot ######
+RUN curl -L $ROBOT_JAR -o /tools/robot.jar &&\
+    curl -L https://raw.githubusercontent.com/ontodev/robot/$ROBOT/bin/robot -o /tools/robot && \
+    chmod +x /tools/robot && \
+    chmod +x /tools/robot.jar
+  
+ENV PATH "/tools/:$PATH"
+
+###### obographviz #####
+RUN cd /tools \
+&& git clone 'https://github.com/cmungall/obographviz.git' \
+&& cd obographviz \
+&& git checkout b0d8f64517d4ae0085072866aaadb7602f41acf7 \
+&& make install
+ENV PATH "/tools/obographviz/bin:$PATH"

requirements.txt

@@ -2,3 +2,4 @@ pandas
 SPARQLWrapper
 rdflib
 openpyxl
+requests

src/run.sh

@@ -9,4 +9,4 @@
 # we therefore map the whole repo (../..) to a docker volume.
 #
 # See README-editors.md for more details.
-docker run -v $PWD/../:/work -w /work/src/ -e ROBOT_JAVA_ARGS='' -e JAVA_OPTS='' --rm -ti obolibrary/odkfull "$@"
+docker run -v $PWD/../:/work -w /work/src/ -e ROBOT_JAVA_ARGS='' -e JAVA_OPTS='' --rm -ti anitacaron/ccf-tools-dep "$@"