From 394e6afe46c7359f3e53753b15fae8c16d62f272 Mon Sep 17 00:00:00 2001
From: korseby <kristian@funkel.ipb-sub.ipb-halle.de>
Date: Fri, 8 Apr 2016 10:15:47 +0200
Subject: [PATCH 1/6] replaced oracle-java with openjdk

---
 Dockerfile | 10 ++--------
 1 file changed, 2 insertions(+), 8 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 1a50d76..8f076a5 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -4,6 +4,8 @@ MAINTAINER Kristian Peters <kpeters@ipb-halle.de>
 
 LABEL Description="Install nmrML in Docker."
 
+
+
 # Update & upgrade sources
 RUN apt-get -y update
 RUN apt-get -y dist-upgrade
@@ -13,10 +15,6 @@ RUN apt-get -y install build-essential software-properties-common
 RUN apt-get install -y byobu curl git htop man unzip vim wget
 
 # Install Java
-RUN echo oracle-java7-installer shared/accepted-oracle-license-v1-1 select true | debconf-set-selections
-#RUN add-apt-repository -y ppa:webupd8team/java
-#RUN apt-get -y update
-#RUN apt-get -y install oracle-java7-installer
 RUN apt-get -y install openjdk-7-jdk openjdk-7-jre
 
 # Clean up
@@ -34,10 +32,6 @@ ADD nmrMLconv.sh /usr/local/bin/nmrMLconv
 RUN mkdir /usr/local/share/nmrML
 RUN install -m755 bin/converter.jar /usr/local/share/nmrML/
 
-# Set JAVA_HOME
-#ENV JAVA_HOME /usr/lib/jvm/java-7-oracle
-#ENV JAVA_HOME /usr/lib/jvm/default-java
-
 # Define data directory
 RUN mkdir /data
 WORKDIR /data

From 77fb6b75a676142c12a0bea0848ebab49f54fb4f Mon Sep 17 00:00:00 2001
From: korseby <kristian@funkel.ipb-sub.ipb-halle.de>
Date: Wed, 18 May 2016 10:08:42 +0200
Subject: [PATCH 2/6] "PhenoMeNalized"

---
 Dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 8f076a5..97eadba 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,8 +1,8 @@
 FROM ubuntu:trusty
 
-MAINTAINER Kristian Peters <kpeters@ipb-halle.de>
+MAINTAINER PhenoMeNal-H2020 Project <phenomenal-h2020-users@googlegroups.com>
 
-LABEL Description="Install nmrML in Docker."
+LABEL Description="Convert NMR-RAW vendor files to nmrML."
 
 
 

From 184d04db00ccb974752aaf5ce0c853894bbafc43 Mon Sep 17 00:00:00 2001
From: korseby <kristian@funkel.ipb-sub.ipb-halle.de>
Date: Mon, 20 Jun 2016 13:48:51 +0200
Subject: [PATCH 3/6] better streamline + documentation

---
 Dockerfile   |  4 ++--
 README.md    | 23 ++++++++++++++++++++++
 _build.sh    |  4 ++--
 _run.sh      | 55 ----------------------------------------------------
 nmrMLconv.sh |  7 -------
 5 files changed, 27 insertions(+), 66 deletions(-)
 create mode 100644 README.md
 delete mode 100755 _run.sh
 delete mode 100755 nmrMLconv.sh

diff --git a/Dockerfile b/Dockerfile
index 97eadba..966487f 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -28,7 +28,6 @@ RUN git clone https://github.com/nmrML/nmrML
 WORKDIR /usr/src/nmrML/tools/Parser_and_Converters/Java/converter
 RUN install -m755 bin/nmrMLcreate /usr/local/bin
 RUN install -m755 bin/nmrMLproc /usr/local/bin
-ADD nmrMLconv.sh /usr/local/bin/nmrMLconv
 RUN mkdir /usr/local/share/nmrML
 RUN install -m755 bin/converter.jar /usr/local/share/nmrML/
 
@@ -36,5 +35,6 @@ RUN install -m755 bin/converter.jar /usr/local/share/nmrML/
 RUN mkdir /data
 WORKDIR /data
 
-ENTRYPOINT ["sh","/usr/local/bin/nmrMLconv"]
+ENTRYPOINT [ "java", "-cp", "./", "-jar", "/usr/local/share/nmrML/converter.jar" ]
+
 
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..f14346d
--- /dev/null
+++ b/README.md
@@ -0,0 +1,23 @@
+# nmrML convert Docker Buildfile
+
+[nmrML](http://nmrml.org/) is an open mark-up language for NMR data. This project contains files that are needed to use the tools to convert RAW vendor NMR files to nmrML files in Docker.
+
+## Building the Docker image
+
+`docker build --tag="phnmnl/nmrmlconv:latest" .`
+
+## Using the Docker image
+
+This examples uses one of the RAW files included in MTBLS1, which you get when you clone the [nmrML-github repository](https://github.com/nmrML/nmrML/) to /usr/src.
+
+`docker run -ti -v /usr/src/nmrML/examples/MTBLS1/FIDs/ADG10003u_007/10/:/src
+		 -v $PWD:/data phnmnl/nmrmlconv:latest
+		 -l create
+		 -b -z -t bruker
+		 -i /src/
+		 -o /data/ADG10003u_007_10.nmrml`
+
+## Galaxy usage
+
+A rudimentary Galaxy node description is included as `nmrmlconv.xml` will be added soon. 
+
diff --git a/_build.sh b/_build.sh
index de33912..01fb15a 100755
--- a/_build.sh
+++ b/_build.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 # Name
-NAME="nmrml"
+NAME="phnmnl/nmrmlconv"
 
 # CPU options
 #CPU_SHARES="--cpu-shares=8"
@@ -10,5 +10,5 @@ NAME="nmrml"
 #MEM="--memory=24g"
 
 # Build docker
-docker build --rm=true $CPU_SHARES $CPU_SETS $CPU_MEMS $MEM --tag=$NAME .
+docker build $CPU_SHARES $CPU_SETS $CPU_MEMS $MEM --tag=$NAME .
 
diff --git a/_run.sh b/_run.sh
deleted file mode 100755
index 1ade1e9..0000000
--- a/_run.sh
+++ /dev/null
@@ -1,55 +0,0 @@
-#!/bin/bash
-
-# Make sure to add the following entry in /etc/default/grub:
-#GRUB_CMDLINE_LINUX="cgroup_enable=memory swapaccount=1"
-
-# Name
-NAME="nmrml"
-
-# CPU options
-#CPU_SHARES="--cpu-shares=8"
-#CPU_SETS="--cpuset-cpus=0-$[$CPU_SHARES-1]"
-#CPU_MEMS="--cpuset-mems=0"
-#MEM="--memory=8g"
-
-# Ports
-#PUBLISH="--publish=8080:80"
-
-# Volumes
-#VOL="--volume=/vol/R/shiny/srv/shiny-server/MetFam:/vol/R/shiny/srv/shiny-server/MetFam:ro"
-
-# Run docker
-docker run ${PUBLISH} --log-driver=syslog $VOL $CPU_SHARES $CPU_SETS $CPU_MEMS $MEM --name="${NAME}-run" -i -t -d $NAME
-
-
-
-# Detach/Attach docker
-# detach: CTRL-P + CTRL-Q
-
-# Start and attach docker (you can also use docker start -ai instead)
-#docker start ${NAME}-run
-#docker attach ${NAME}-run
-
-# Start shell inside running docker
-#docker exec -i -t ${NAME}-run /bin/bash
-
-# Start failed container with different entrypoint
-#docker run -ti --entrypoint=/bin/bash ${NAME}-run
-
-# Commit changes locally
-#docker commit ${NAME}-run
-
-# Show docker container and images
-#docker ps -a
-#docker images
-
-# Delete container and image
-#docker rm ${NAME}-run
-#docker rmi ${NAME}
-
-# Delete exited containers
-#docker rm $(docker ps -a -f status=exited | grep -v CONTAINER\ ID | awk '{print $1}')
-
-# Delete intermediate/untagged images
-#docker rmi $(docker images | grep '^<none>' | awk '{print $3}')
-
diff --git a/nmrMLconv.sh b/nmrMLconv.sh
deleted file mode 100755
index 14f1a60..0000000
--- a/nmrMLconv.sh
+++ /dev/null
@@ -1,7 +0,0 @@
-#!/bin/bash
-JAVA="java"
-NMRML_DIR="/usr/local/share/nmrML"
-CONVERTER="$JAVA -cp ./ -jar $NMRML_DIR/converter.jar"
-
-$CONVERTER $i*
- 

From 526977bcf7462706367ac474ee38321e1c5ac456 Mon Sep 17 00:00:00 2001
From: korseby <kristian@funkel.ipb-sub.ipb-halle.de>
Date: Tue, 21 Jun 2016 09:23:56 +0200
Subject: [PATCH 4/6] added galaxy xml tool description

---
 nmrmlconv.xml | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 nmrmlconv.xml

diff --git a/nmrmlconv.xml b/nmrmlconv.xml
new file mode 100644
index 0000000..a063a4a
--- /dev/null
+++ b/nmrmlconv.xml
@@ -0,0 +1,35 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
+<!--Proposed Tool Section: [File Handling]-->
+<tool id="nmrmlconv" name="nmrmlconv" version="0.1">
+  <requirements>
+    <container type="docker">phnmnl/nmrmlconv</container>
+  </requirements>
+  <description>Converts vendor RAW NMR to nmrML.</description>
+  <command>
+     java -cp ./ -jar /usr/local/share/nmrML/converter.jar -l create -b -z -t $venformat -i $infile -o $outfile
+  </command>
+  <inputs>
+    <param name="infile" type="data" format="data" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" optional="False" label="Input file to convert" />
+    <param name="venformat" type="select" value="" optional="True" label="Vendor format" help="Choose the right vendor format.">
+      <option value="bruker" selected="True">Bruker</option>
+      <option value="varian">Varian</option>
+      <option value="jeol">Jeol</option>
+      <option value="tecmag">TecMag</option>
+      <option value="nmrstar">NMR Star</option>
+      <option value="chemmagnetics">ChemMagnetics</option>
+      <option value="geomega">GE Omega</option>
+      <option value="galactic">Galactic</option>
+      <option value="jcamp">JCAMP</option>
+      <option value="lybrics">Lybrics</option>
+      <option value="nuts">Nuts</option>
+      <option value="nicolet">Nicolet</option>
+      <option value="netcdf">netCDF</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="nmrML" name="outfile" label="nmrML file" />
+  </outputs>
+  <help>nmrML is an open mark-up language for NMR data. This tool converts RAW vendor NMR data to nmrML format.
+  </help>
+</tool>

From 6c326f421c8a5893c094107c010383f53ff2aaab Mon Sep 17 00:00:00 2001
From: korseby <kristian@funkel.ipb-sub.ipb-halle.de>
Date: Tue, 21 Jun 2016 09:25:09 +0200
Subject: [PATCH 5/6] updated readme for galaxy integration

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index f14346d..44a2242 100644
--- a/README.md
+++ b/README.md
@@ -19,5 +19,5 @@ This examples uses one of the RAW files included in MTBLS1, which you get when y
 
 ## Galaxy usage
 
-A rudimentary Galaxy node description is included as `nmrmlconv.xml` will be added soon. 
+A rudimentary Galaxy node description is included as `nmrmlconv.xml`.
 

From cb3fd031ad0868f266689c96e26befa9dbf3b93c Mon Sep 17 00:00:00 2001
From: Pierrick Roger Mele <pierrick.rogermele@cea.fr>
Date: Wed, 20 Jul 2016 14:48:35 +0200
Subject: [PATCH 6/6] Add advise for building under macOS.

---
 README.md | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/README.md b/README.md
index 44a2242..d10f029 100644
--- a/README.md
+++ b/README.md
@@ -6,6 +6,11 @@
 
 `docker build --tag="phnmnl/nmrmlconv:latest" .`
 
+Under macOS, you may encounter a `no space left on device` error, in which case you will have to create a docker machine with enough memory:
+```bash
+docker-machine create -d virtualbox --virtualbox-memory 2048 my_new_docker_machine
+```
+
 ## Using the Docker image
 
 This examples uses one of the RAW files included in MTBLS1, which you get when you clone the [nmrML-github repository](https://github.com/nmrML/nmrML/) to /usr/src.