From 05fc1b54ddd08321eda5ee4bed8c3491e1187e8f Mon Sep 17 00:00:00 2001
From: Olivier Filangi <olivier.filangi@inrae.fr>
Date: Mon, 8 Nov 2021 15:06:31 +0100
Subject: [PATCH] 0.1.5 (#23)

* udpate Readme and plugin gpg https://github.com/jodersky/sbt-gpg

* downgrade gpg to 0.2.1. 0.2.2 not available !

* remove tagret directory fro repo

* remove tagret directory fro repo

* update Readme

* fix jar publication

* covered code for commands

* update readme with badge

* remove script

* change galaxy recipe directory

* remove temp file

* minor fix for resume

* add planemo test

* add planemo test

* add planemo test

* add planemo test

* add planemo test

* planemo test only master/main/develop

* lint planemo + conda test version

* lint planemo + conda test version

* lint planemo + conda test version

* update fix meta.yml

* remove conda recipe

* clean repo

* add sbt-release (#16)

* Sbt release (#18)

* add sbt-release

* valid pom generation

* Dockerfile (#20)

* target directory for assembly

* add dockerized task

* add dockerfile

* update gitignore

* use directory docker

* update docker management

* fix outputdir assembly

* update docker config

* remove debug config

* Dockerfile (#22)

* target directory for assembly

* add dockerized task

* add dockerfile

* update gitignore

* use directory docker

* update docker management

* fix outputdir assembly

* update docker config

* remove debug config

* remove coverage enable

* fix dockerfile implementation to run process inside galaxy tools
---
 build.sbt         |  1 -
 docker/Dockerfile | 15 +++++++++------
 docker/p2m2tools  |  4 ++--
 3 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/build.sbt b/build.sbt
index 8d2b82b..df31b65 100644
--- a/build.sbt
+++ b/build.sbt
@@ -26,7 +26,6 @@ libraryDependencies += "com.github.scopt" %% "scopt" % "4.0.1"
 
 // Coverage
 
-coverageEnabled := true
 coverageMinimumStmtTotal := 70
 coverageFailOnMinimum := false
 coverageHighlighting := true
diff --git a/docker/Dockerfile b/docker/Dockerfile
index 1e58f6a..bd6dc0b 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -3,11 +3,9 @@ FROM openjdk:jdk-bullseye
 LABEL author="Olivier Filangi"
 LABEL mail="olivier.filangi@inrae.fr" 
 
-ARG BRANCH=main
+ARG BRANCH=develop
 ARG REPOSITORY_URL=https://github.com/p2m2/p2m2tools.git
 
-USER root
-
 # install sbt:https://www.scala-sbt.org/1.x/docs/Installing-sbt-on-Linux.html
 
 RUN apt update &&\
@@ -22,8 +20,13 @@ RUN apt update &&\
 RUN git clone ${REPOSITORY_URL} /p2m2tools_repo
 
 WORKDIR /p2m2tools_repo
-RUN git checkout ${BRANCH} && sbt assembly
 
-COPY p2m2tools .
 
-ENTRYPOINT [ "./p2m2tools" ]
+RUN git checkout ${BRANCH} && sbt coverageOff assembly
+
+COPY p2m2tools /usr/bin/
+
+RUN apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+
+
diff --git a/docker/p2m2tools b/docker/p2m2tools
index 635b2e9..05bdf72 100755
--- a/docker/p2m2tools
+++ b/docker/p2m2tools
@@ -6,8 +6,8 @@ if [ $# -eq 0 ]
     exit 1
 fi
 
-
-JAR=$(find $PWD/assembly -name "*.jar")
+#  Directory inside Dockerfile should correspond to /p2m2tools_repo directory 
+JAR=$(find /p2m2tools_repo/assembly -name "*.jar")
 
 java -cp $JAR $*