Generating KNIME Nodes for External Tools


You can download it from the KNIME Download Site. We will use Version 2.8. (We assume that you have installed it to $HOME/eclipse_knime_2.8.0).
For Downloading the latest samtools and GenericKnimeNodes.
Apache Ant
The Generic KNIME Plugins project uses Apache Ant as the build system. On Linux and Mac, you should be able to install it through your package manager. For Windows, see the Apache Ant Downloads (note that samtools does not work on Windows so you will not be able to follow through with this tutorial on Windows).

Running Example

We will adapt some functions from the samtools package to KNIME:

This tool will execute samtools view -o ${OUT} ${IN}.
This tool will execute samtools view -Sb -o ${OUT} ${IN}.
This tool will execute samtools sort -f -o ${OUT} ${IN}.


The -f flag is required for the integration of samtools without a wrapper, since it would append .bam to ${OUT} for getting the output name. However, only the current trunk version from the samtools GitHub project supports this flag.

Preparation: Building samtools and Downloading GenericKnimeNodes

As mentioned above, we have to build the current trunk version of samtools for the sort_bam tool to work. The following shell commands download the current samtools trunk from GitHub and build samtools. We will work in a new directory knime_samtools (we will assume that the directory is directly in your $HOME for the rest of the tutorial.

knime_samtools # git clone
knime_samtools # cd samtools
samtools # make
samtools # ls -l samtools
-rwxr-xr-x 1 user group 1952339 May  7 16:36 samtools
samtools # cd ..
knime_samtools #

Then, we need to download GenericKnimeNodes:

knime_samtools # git clone git://

Preparation: Installing KNIME File Handling

We need to install support for file handling nodes in KNIME. For this, open the window for installing Eclipse plugins; in the program’s main menu: Help > Install New Software....

Here, enter into the Work with: field, enter file into the search box, and finally select KNIME File Handling Nodes in the list. Then, click Next and follow through with the installation of the plugin. When done, Eclipse must be restarted.



KNIME nodes are shipped as Eclipse plugins. The GenericKnimeNodes (GWN) package provides the infrastructure to automatically generate such nodes from the description of their command line. The description of the command line is kept in XML files called Common Tool Descriptor (CTD) files. The input of the GWN package is a directory tree with the following structure:

  ├── descriptors (place your ctd files and mime.types here)
  ├── payload (place your binaries here)
  ├── icons (the icons to be used must be here)
  ├── DESCRIPTION (A short description of the project)
  ├── LICENSE (Licensing information of the project)
  └── COPYRIGHT (Copyright information of the project)
File with the plugin configuration.
Directory with the CTD files and a mime.types file. This mime.types file contains a mapping between MIME types and file extensions. There is one CTD file called ${app_name}.ctd.
ZIP archives with the binaries are located here. This directory has to be present even if the directory is empty. Also, you need a file binaries.ini in this directory which can be empty or contain environment variable definitions as name=value lines.
Some icons: A file category.png (15x15 px) for categories in the KNIME tool tree. A file splash.png (50x50 px) with an icon to display in the KNIME splash screen. One for each app, called ${app_name}.png.
A text file with your project’s description.
A file with the license of the project.
A file with copyright information for the project.

The GWN project provides tools to convert such a plugin directory into an Eclipse plugin. This plugin can then be launched together with KNIME. The following picture illustrates the process.


Obtaining the Demo Workflow Plugin Directory

Please download the file and look around in the archive. Also have a look into binaries_*_*.zip files in payload. The structure of this ZIP file is explained below in Anatomy of a Plugin Directory.

Creating an Exclipse Plugin from the Plugin Directory

The next step is to use GKN to create an Eclipse plugin from the workflow plugin directory. For this, change to the directory GenericKnimeNodes that we cloned using git earlier. We then execute ant and pass the variables knime.sdk with the path to the KNIME SDK that you downloaded earlier and plugin.dir with the path of our plugin directory.

knime_samtools # cd GenericKnimeNodes
GenericKnimeNodes # ant -Dknime.sdk=${HOME}/eclipse_knime_2.8.0 \

This generates an Eclipse plugin with wrapper classes for our nodes. The generated files are within the generated_plugin directory of the directory GenericKnimeNodes.

Importing the Generated Projects into Eclipse

In the main menu File > Import.... In the Import window, select General > Existing Project Into Workspace


In the next dialog, click Browse... next to Select root directory.


Then, select the directory of your “GenericWorkflowNodes” checkout. The final dialog should then look as follows.

Clicking finish will import (1) the GKN classes themselves and (2) your generated plugin’s classes.


Now, the packages of the GKN classes and your plugin show up in the left Package Explorer pane of Eclipse.



Information: Synchronizing ant build result with Eclipse.

Since the code generation happens outside of Eclipse, there are often problems caused by Eclipse not recognizing updates in generated .java files. After each call to ant, you should clean all built files in all projects by selecting the menu entries Project > Clean..., selecting Clean all projects, and then clicking OK.

Then, select all projects in the Package Explorer, right-click and select Refresh.

Launching Eclipse with our Nodes

Finally, we have to launch KNIME with our plugin. We have to create a run configuration for this. Select Run > Run Configurations....

In the Run Configurations window, select Eclipse Application on the left, then create the small New launch configuration icon on the top left (both marked in the following screenshot). Now, set the Name field to “KNIME”, select Run an application and select org.knime.product.KNIME_APPLICATION in the drop down menu. Finally, click Run.


Your tool will show up in the tool selector in community/SAM and BAM.


Here is an example KNIME workflow with the nodes that we just created.


Anatomy of a Plugin Directory

You can download a ZIP archive of the resulting project from the attached file We will ignore the contents of icons, DESCRIPTION, LICENSE, and COPYRIGHT here. You can see all relevant details by inspecting the ZIP archive.

The file

The content of the file is as follows:

# the package of the plugin

# the name of the plugin

# the version of the plugin

# the path (starting from KNIMEs Community Nodes node)


When creating your own plugin directory, you only have to update the first three properties:

A Java package path to use for the Eclipse package.
A CamelCase name of the plugin.
Version of the Eclipse plugin.

The file descriptors/mime.types

The contents of the file is as shown below. Each line contains the definition of a MIME type. The name of the mime type is followed (separated by a space) by the file extensions associated with the file type. There may be no ambiguous mappings, i.e. giving the extension for both application/x-fasta and application/x-fastq.

application/x-fasta fa fasta
application/x-fastq fq fastq
application/x-sam sam
application/x-bam bam

The file descriptors/samtools_sort_bam.ctd

This file descripes the SortBam tool for sorting BAM files. We do not describe the files descriptors/samtools_sam_to_bam.ctd and descriptors/samtools_bam_to_sam.ctd in the same detail as you can interpolate from here.

<?xml version="1.0" encoding="UTF-8"?>
<tool name="SortBam" version="0.1.17" category="SAM and BAM"
    <description><![CDATA[SAMtools BAM Sorting.]]></description>
    <manual><![CDATA[samtools sort]]></manual>
    <docurl>Direct links in docs</docurl>
        <clielement optionIdentifier="sort" isList="false" />
        <clielement optionIdentifier="-f" isList="false" />

        <!-- Following clielements are arguments. You should consider
             providing a help text to ease understanding. -->
        <clielement optionIdentifier="" isList="false">
            <mapping referenceName="bam_to_sam.argument-0" />
        <clielement optionIdentifier="" isList="false">
            <mapping referenceName="bam_to_sam.argument-1" />

        <clielement optionIdentifier="" isList="false">
            <mapping referenceName="bam_to_sam.argument-2" />
    <PARAMETERS version="1.4"
        <NODE name="bam_to_sam" description="SAMtools BAM to SAM conversion">
            <ITEM name="argument-0" value="" type="input-file" required="true"
                  description="Input BAM file." supported_formats="*.bam" />
            <ITEM name="argument-1" value="" type="output-file" required="true"
                  description="Output BAM file." supported_formats="*.bam" />
            <ITEM name="argument-2" value="" type="string" required="true"
                  description="Sort by query name (-n) instead of position (default)" restrictions=",-n" />

Here is a description of the tags and the attributes:

The root tag.
The CamelCase name of the tool as shown in KNIME and part of the class name.
The version of the tool.
The path to the tool’s category.
The name of the executable in the payload ZIP’s bin dir.
Description of the tool.
Long description for the tool.
URL to the tool’s documentation.
Container for the <clielement> tags. These tags describe the command line options and arguments of the tool. The command line options and arguments can be mapped to parameters which are configurable through the UI. The parameters are stored in tool/PARAMETERS
There is one entry for each command line argument and option.
The identifier of the option on the command line. For example, for the -l option of ls, this is -l.
Whether or not the parameter is a list and multiple values are possible. One of true and false.
Provides the mapping between a CLI element and a PARAMETER.
The path of the parameter. The parameters <ITEM> s in tool/PARAMETERS are stored in nested <NODE> tags and this gives the path to the specific parameter.
Container for the <NODE> and <ITEM> tags. The <PARAMETERS> tag is in a diferent namespace and provides its own XSI.
Format version of the <PARAMETERS> section.
A node in the parameter tree. You can use such nodes to organize the parameters in a hierarchical fashion.
Boolean that marks an option as advanced.
Name of the parameter section.
Documentation of the parameter section.
Description of one command line option or argument.
Name of the option.
Default value of the option. When a default value is given, it is passed to the program, regardless of whether the user touched the default value or not.
Type of the parameter. Can be one of string, int, double, input-file, output-path, input-prefix, or output-prefix. Booleans are encoded as string with the restrictions attribute set to "true,false".
Boolean that states whether the parameter is required or not.
Documentation for the user.
A list of supported file formats. Example: "*.bam,*.sam".
In case of int or double types, the restrictions have the form min:, :max, min:max and give the smallest and/or largest number a value can have. In the case of string types, restrictions gives the list of allowed values, e.g. one,two,three. If the type is string and the restriction field equals "true,false", then the parameter is a boolean and set in case true is selected in the GUI. A good example for this would be the -l flag of the ls program.


If a <clielement> does provides an empty <tt>optionIdentifier</tt> then it is a positional argument without a flag (examples for parameters with flags are -n 1, --number 1).

If a <clielement> does not provide a <mapping> then it is passed regardless of whether has been configured or not.

The samtools_sort_bam tool from above does not provide any configurable options but only two arguments. These are by convention called argument-0 and argument-1 but could have any name.

Also, we always call the program with view -f as the first two command line arguments since we do not provide a mapping for these arguments.

The directory payload

The directory payload contains ZIP files with the executable tool binaries. There is one ZIP file for each platform (Linux, Windows, and Mac Os X) and each architecture (32 bit and 64 bit). The names of the files are binaries_${plat}_${arch}.zip where ${plat} is one of lnx, win, or mac, and ${arch} is one of 32 and 64.

Each ZIP file contains a directory /bin which is used as the search path for the binary given by <executableName>. Also, it provides an INI file /binaries.ini which can be used to define environment variables to set before executing any tools.

The ZIP file can also provide other files in directories such as /share.

Generating KNIME Nodes for SeqAn Apps

You can generate a workflow plugin directory for the SeqAn apps using the prepare_workflow_plugin target. Then, you can generate the Knime Nodes/Eclipse plugins as described above using ant.

~ # svn co seqan-trunk
~ # mkdir -p seqan-trunk-build/release
~ # seqan-trunk-build/release
release # cmake ../../seqan-trunk
release # make prepare_workflow_plugin
release # cd ~/knime_samtools/GenericKnimeNodes
GenericKnimeNodes # ant -Dknime.sdk=${HOME}/eclipse_knime_2.8.0 \
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