README update

Dockerfile

@@ -1,8 +1,10 @@
 FROM ubuntu:trusty
 
-MAINTAINER Kristian Peters <kpeters@ipb-halle.de>
+MAINTAINER PhenoMeNal-H2020 Project <phenomenal-h2020-users@googlegroups.com>
+
+LABEL Description="Convert NMR-RAW vendor files to nmrML."
+
 
-LABEL Description="Install nmrML in Docker."
 
 # Update & upgrade sources
 RUN apt-get -y update
@@ -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
@@ -30,17 +28,13 @@ 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/
 
-# 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
 
-ENTRYPOINT ["sh","/usr/local/bin/nmrMLconv"]
+ENTRYPOINT [ "java", "-cp", "./", "-jar", "/usr/local/share/nmrML/converter.jar" ]
+
 

README.md

@@ -0,0 +1,28 @@
+# 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" .`
+
+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.
+
+`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`.
+

_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 .
 

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>