From 4dff5fe62a3b6676e897829ccf2e885f6065dc1a Mon Sep 17 00:00:00 2001
From: Dave Roe <roex0050@umn.edu>
Date: Thu, 1 Sep 2022 08:30:36 -0500
Subject: [PATCH] Continuing previous checkin, use sdkman for installing
 groovy.

---
 Dockerfile | 48 ++++++++++++++++++++++++++++++------------------
 1 file changed, 30 insertions(+), 18 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 5db14c0..cf349ad 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,20 +1,17 @@
 FROM ubuntu:latest
 MAINTAINER Dave Roe
 
-# apt stuff
+# general installs
 RUN apt-get update \
-  && apt-get install -qyy curl git make vim cmake zip \
-     gcc g++ unzip subversion gzip openjdk-17-jdk openjdk-17-doc wget \
-     zlib1g-dev gnuplot \
-     bzip2 libbz2-dev liblzma-dev libncurses5-dev libncursesw5-dev \
-  && apt-get clean
+  && apt-get install -qyy curl git make vim cmake \
+     gcc g++ zip unzip subversion gzip wget \
+     zlib1g-dev gnuplot openjdk-17-jdk openjdk-17-doc \
+     bzip2 libbz2-dev liblzma-dev libncurses5-dev libncursesw5-dev
+ENV JAVA_HOME /usr/lib/jvm/java-17-openjdk-amd64/
 
-# install stuff
+# install general stuff
 ENV TMPDIR /tmp
 RUN mkdir -p /opt/bin && cd /opt/bin \
-  && wget -qO- http://get.nextflow.io | bash \
-  && sed -i s/"curl -fsSL"/"curl -fsSLk"/ /opt/bin/nextflow \
-  && chmod 755 /opt/bin/nextflow \
   && wget https://github.com/refresh-bio/KMC/releases/download/v3.2.1/KMC3.2.1.linux.tar.gz \
   && gunzip KMC3.2.1.linux.tar.gz && tar -xvf KMC3.2.1.linux.tar && rm -f KMC3.2.1.linux.tar \
   && mv bin/* . && rmdir bin \
@@ -22,13 +19,28 @@ RUN mkdir -p /opt/bin && cd /opt/bin \
   && cd /opt/jars \
   && wget http://www.apache.org/dist/commons/math/binaries/commons-math3-3.6.1-bin.tar.gz \
   && tar -zxvf commons-math3-3.6.1-bin.tar.gz \
-  && rm -f /opt/jars/commons-math3-3.6.1-bin.tar.gz \
-  && curl -s get.sdkman.io | bash \
-  && source "/root/.sdkman/bin/sdkman-init.sh" \
-  && sdk install groovy
-  
+  && rm -f /opt/jars/commons-math3-3.6.1-bin.tar.gz 
+
+# install groovy with sdkman
+# https://stackoverflow.com/questions/53656537/install-sdkman-in-docker-image
+RUN mv /bin/sh /bin/sh.bak && ln -s /bin/bash /bin/sh
+ENV SDKMAN_DIR /usr/local/sdkman
+RUN set -x \
+    && apt-get update \
+    && apt-get install -y unzip --no-install-recommends \
+    && rm -rf /var/lib/apt/lists/*
+RUN curl -s get.sdkman.io | bash \
+ && chmod 700 /usr/local/sdkman/bin/sdkman-init.sh 
+RUN source "/usr/local/sdkman/bin/sdkman-init.sh" \
+ && sdk install groovy  \
+ && rm -f /bin/sh && mv /bin/sh.bak /bin/sh
+ENV GROOVY_HOME /usr/local/sdkman/candidates/groovy/current/
+
+RUN cd /opt/bin && wget -qO- http://get.nextflow.io | bash \
+  && sed -i s/"curl -fsSL"/"curl -fsSLk"/ /opt/bin/nextflow \
+  && chmod 755 /opt/bin/nextflow
+
 # google guava
-ENV JAVA_HOME /usr/lib/jvm/java-17-openjdk-amd64
 RUN cd /opt/jars \
   && wget https://repo1.maven.org/maven2/com/google/guava/guava/31.1-jre/guava-31.1-jre.jar \
   && chmod 755 guava-31.1-jre.jar
@@ -37,8 +49,8 @@ RUN cd /opt/jars \
 ENV NXF_OPTS "-Xms4G -Xmx50G"
 ENV JAVA_OPTS "-Xms4G -Xmx50G"
 ENV LD_LIBRARY_PATH /opt/lib:$LD_LIBRARY_PATH
-ENV PATH /opt/bin:/opt/kpi:$PATH
-ENV CLASSPATH /opt/jars/guava-31.1-jre.jar:/opt/jars/commons-math3-3.6.1/commons-math3-3.6.1.jar:/usr/share/groovy/lib/commons-cli.jar:$CLASSPATH
+ENV PATH /opt/bin:/opt/kpi:$JAVA_HOME/bin:$GROOVY_HOME/bin:$PATH
+ENV CLASSPATH /opt/jars/guava-31.1-jre.jar:/opt/jars/commons-math3-3.6.1/commons-math3-3.6.1.jar:$GROOVY_HOME/lib/commons-cli.jar:$CLASSPATH
 
 # kpi files
 RUN cd /opt && git clone https://github.com/droeatumn/kpi.git