diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 0000000000000000000000000000000000000000..45c917cf0d91d9cff8af9554725a61116e2bb974
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1,5 @@
+.gitlab-ci
+Dockerfile
+.dockerignore
+models
+.git
diff --git a/Dockerfile b/Dockerfile
index 0c18c673d8924fddd6264f5694105f2867573fab..7656ba4802059e83b27a3e9e28ddc9ee5a1e2047 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -22,21 +22,20 @@ RUN apt-get update -y && apt-get install -y \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
-COPY trainbenchmark-reporting/install.R /trainbenchmark/trainbenchmark-reporting/install.R
+COPY trainbenchmark/trainbenchmark-reporting/install.R /trainbenchmark/trainbenchmark-reporting/install.R
RUN Rscript /trainbenchmark/trainbenchmark-reporting/install.R
#USER user
WORKDIR /trainbenchmark
-COPY --chown=user:user . .
+COPY --chown=user:user trainbenchmark/ /trainbenchmark/
+COPY --chown=user:user docker /trainbenchmark/docker
COPY docker/bashrc /home/user/.bashrc
RUN ./gradlew --no-daemon preprocess
RUN ./gradlew --no-daemon build shadowJar -x test
RUN ./gradlew --no-daemon initScripts
-
-
# when benchmarking run:
# RUN ./gradlew --no-daemon generate
# RUN ./gradlew --no-daemon individualInjectBenchmark
diff --git a/docker/bashrc b/docker/bashrc
new file mode 100644
index 0000000000000000000000000000000000000000..146be858b74bbb6bea7f7c57d9f88ddd1a08d6da
--- /dev/null
+++ b/docker/bashrc
@@ -0,0 +1,15 @@
+function csv_viewer {
+ column -t -s, -n "$@" | less -F -S -X -K
+}
+alias configure_default="/trainbenchmark/scripts/configure.sh 1 1024 900 10"
+alias configure_medium="/trainbenchmark/scripts/configure.sh 8 256 60 5"
+alias configure_small="/trainbenchmark/scripts/configure.sh 1 128 20 2"
+
+alias doc_motd="bash /trainbenchmark/docs/motd"
+alias doc_basic="bash /trainbenchmark/docs/basic"
+alias doc_advanced="bash /trainbenchmark/docs/advanced"
+
+alias frogsay="/usr/games/cowsay -f /trainbenchmark/docker/frog.cow"
+alias frogsay_tip="shuf -n 1 /trainbenchmark/docker/tips | frogsay"
+
+doc_motd
diff --git a/docker/frog.cow b/docker/frog.cow
new file mode 100644
index 0000000000000000000000000000000000000000..7ab944d97e6126780cd14ffb69201805aa1e38c8
--- /dev/null
+++ b/docker/frog.cow
@@ -0,0 +1,28 @@
+$the_cow =<<"EOC"
+ $thoughts
+ ___ _--_
+ / - / \\
+ ( OOO \\ ( @@ )
+ | OOO _;\\-/| @@@_|
+ \\___/######\\___/\\
+ /##############\\
+ / ###### ## #|
+ / ##@##@## |
+ / ###### ## \\
+ <______-------___\\ . //_
+ | ____ | | //# \\__~__
+ \\ $tongue \\ //### \\ \\
+ | /\' ## ## ##\\ __--~--_
+ \\_________- /\\ ) ^ ##|--########\\
+ /--~-_\\________/_ | #@##|#######Y##|
+ | \\ ` /| /O/ ( ### \') ##/######/###/
+ \\ \\ | | -- | ### /LLLLL--###/
+ \\_ \\/ | \\_ \\ ) /####_____--
+ ___ / \\ / | _-####\\
+(___/ -\\_________/ / -- |#####@@@@@@\'_
+ (__\\_ __,) (.___ ,/ /##### `@@
+ | -\\\\- //-// @@ @@@@@.
+ | | \\\\_ _// // @\' \'@@.
+ (.) \\_) / / // @@@
+ (_) (_\'
+EOC
diff --git a/docker/tips b/docker/tips
new file mode 100644
index 0000000000000000000000000000000000000000..8ba4f05f86f90ad9fdceeaebd238937943117747
--- /dev/null
+++ b/docker/tips
@@ -0,0 +1,7 @@
+Did you know? You can use "doc_motd" to display the login message
+Use "doc_basic" to display the basic commands to run the benchmark
+Use "doc_advanced" to see advanced configuration
+Use "csv_view" to get a nicely formatted output of csv files
+I am the Fog Frog
+What the Fog?
+Use "./scripts/configure.sh" to change problem sizes. Some defaults are also inside the commands "configure_default", "configure_medium", "configure_small"
diff --git a/trainbenchmark/docs/advanced b/trainbenchmark/docs/advanced
new file mode 100644
index 0000000000000000000000000000000000000000..5c0159e23a1a09823e8c1a8cbd3bd9ea5603af61
--- /dev/null
+++ b/trainbenchmark/docs/advanced
@@ -0,0 +1,21 @@
+#!/bin/bash
+echo -e "\033[1;91mAdvanced Configuration:"
+echo -e ""
+echo -e "\033[1;91mCoarse Configuration"
+echo -e "\033[0mUse the ./scripts/configure.sh command or configure_small or configure_medium or configure_default"
+echo -e ""
+echo -e "\033[1;91mGeneration of test-models"
+echo -e "\033[0mFor example to change the maxSize option. Can be configured inside:"
+echo -e "* trainbenchmark-scripts/src-template/GeneratorScript.groovy"
+echo -e "When you are finished, run:"
+echo -e "* ./gradlew initScripts"
+echo -e "* ./gradlew generate"
+echo -e ""
+echo -e "\033[1;91mBenchmarking"
+echo -e "\033[0mCan be configured inside:"
+echo -e "* trainbenchmark-scripts/src-template/IndividualBenchmarkInjectScript.groovy"
+echo -e "* trainbenchmark-scripts/src-template/IndividualBenchmarkRepairScript.groovy"
+echo -e "When you are finished, run:"
+echo -e "* ./gradlew initScripts"
+echo -e "* ./gradlew individualInjectBenchmark"
+echo -e "* ./gradlew individualRepairBenchmark"
diff --git a/trainbenchmark/docs/basic b/trainbenchmark/docs/basic
new file mode 100644
index 0000000000000000000000000000000000000000..4daa18a5ccd3c79cd9cd04945251569557697746
--- /dev/null
+++ b/trainbenchmark/docs/basic
@@ -0,0 +1,11 @@
+#!/bin/bash
+echo -e "\033[1;96mQuick Start"
+echo -e "\033[0m* configure_small"
+echo -e "* ./gradlew generate # will generate the test-models in default settings takes ~40gb"
+echo -e "* ./gradlew individualInjectBenchmark"
+echo -e "* ./gradlew individualRepairBenchmark"
+echo -e ""
+echo -e "\033[1;96mReading the Benchmark results"
+echo -e "\033[0mResults of individualInjectBenchmark and individualRepairBenchmark are stored inside:"
+echo -e "* XXXX for graphs"
+echo -e "* XXXX for csv - use command: csv_viewer data.csv"
diff --git a/trainbenchmark/docs/motd b/trainbenchmark/docs/motd
new file mode 100644
index 0000000000000000000000000000000000000000..8cd2dfe9e66dfb60509b035dc444c92ae13df650
--- /dev/null
+++ b/trainbenchmark/docs/motd
@@ -0,0 +1,21 @@
+#!/bin/bash
+# echo -e " "
+# echo -e " * ) ) ) ) "
+# echo -e " ) /( ( ) ( ( /( ( ( /( ) ) ( ( /( "
+# echo -e " ( )(_)))( ( /( )\ ( )\()) ))\ ( ( )\()) ( ( /( )( )\()) "
+# echo -e "(_(_())(()\ )(_))((_) )\ ) ((_)\ /((_) )\ ) )\ ((_)\ )\ ' )(_))(()\ ((_)\ "
+# echo -e "|_ _| ((_)((_)_ (_) _(_/( | |(_)(_)) _(_/( ((_)| |(_) _((_)) ((_)_ ((_)| |(_) "
+# echo -e " | | | '_|/ _' | | || ' \))| '_ \/ -_)| ' \))/ _| | ' \ | ' \()/ _' || '_|| / / "
+# echo -e " |_| |_| \__,_| |_||_||_| |_.__/\___||_||_| \__| |_||_||_|_|_| \__,_||_| |_\_\ "
+# echo -e " "
+echo "Welcome to the Trainbenchmark! I'll be your guide.. just type frogsay_tip" | /usr/games/cowsay -f /trainbenchmark/docker/frog.cow
+#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null && pwd )"
+#bash $DIR/basic
+echo -e ""
+echo -e "\033[1;96mDocumentation"
+echo -e "\033[0mRun the following commands"
+echo -e "* doc_motd # displays this message"
+echo -e "* doc_basic # displays the basic guide"
+echo -e "* doc_advanced # displays the advanced guide"
+echo -e ""
+# bash $DIR/advanced
diff --git a/trainbenchmark/scripts/configure.sh b/trainbenchmark/scripts/configure.sh
new file mode 100644
index 0000000000000000000000000000000000000000..fb3a9d59b65c10bcaf509cf2965fc7ca89b8242b
--- /dev/null
+++ b/trainbenchmark/scripts/configure.sh
@@ -0,0 +1,37 @@
+#!/bin/bash
+
+cd "$( cd "$( dirname "$0" )" && pwd )/../"||exit 1
+
+MINSIZE="$1"
+MAXSIZE="$2"
+TIMEOUT="$3"
+RUNS="$4"
+
+if [ -z "$RUNS" ]
+then
+ echo "Usage: ./scripts/configure.sh min max timeout runs"
+ echo "Will configure the generateor and benchmark to use problems between sizes min and max"
+ echo "The benchmark receives a timeout in seconds and the amount of runs"
+ echo "Default is: ./scripts/configure.sh 1 1024 900 10"
+ exit 1
+fi
+
+echo -e "\\033[1;96mRemember that this only configures and initializes. Further steps:"
+echo -e "\\033[1;91mGenerate:"
+echo -e "\\033[0m if not yet done run ./gradlew generate"
+echo " maxSize 1024 -> ~40GB of data"
+echo -e "\\033[1;91mBenchmark:"
+echo -e "\\033[0m ./gradlew individualInjectBenchmark"
+echo " ./gradlew individualRepairBenchmark"
+
+sed -i "s/^def minSize =.*/def minSize = $MINSIZE/" ./trainbenchmark-scripts/src-template/GeneratorScript.groovy
+sed -i "s/^def maxSize =.*/def maxSize = $MAXSIZE/" ./trainbenchmark-scripts/src-template/GeneratorScript.groovy
+sed -i "s/^def minSize =.*/def minSize = $MINSIZE/" ./trainbenchmark-scripts/src-template/IndividualBenchmarkInjectScript.groovy
+sed -i "s/^def maxSize =.*/def maxSize = $MAXSIZE/" ./trainbenchmark-scripts/src-template/IndividualBenchmarkInjectScript.groovy
+sed -i "s/^def timeout =.*/def timeout = $TIMEOUT/" ./trainbenchmark-scripts/src-template/IndividualBenchmarkInjectScript.groovy
+sed -i "s/^def runs =.*/def runs = $RUNS/" ./trainbenchmark-scripts/src-template/IndividualBenchmarkInjectScript.groovy
+sed -i "s/^def minSize =.*/def minSize = $MINSIZE/" ./trainbenchmark-scripts/src-template/IndividualBenchmarkRepairScript.groovy
+sed -i "s/^def maxSize =.*/def maxSize = $MAXSIZE/" ./trainbenchmark-scripts/src-template/IndividualBenchmarkRepairScript.groovy
+sed -i "s/^def timeout =.*/def timeout = $TIMEOUT/" ./trainbenchmark-scripts/src-template/IndividualBenchmarkRepairScript.groovy
+sed -i "s/^def runs =.*/def runs = $RUNS/" ./trainbenchmark-scripts/src-template/IndividualBenchmarkRepairScript.groovy
+./gradlew --no-daemon initScripts