Question: Adding custom tools: newbie
gravatar for plindenbaum
3.9 years ago by
plindenbaum90 wrote:

Hi all, I'm learning how to create wrap a java program in my galaxy instance:

<?xml version="1.0"?>
<tool id="my_id" name="my_app" version="my_version" hidden="false">
  <description>My tool</description>
  <command interpreter="bash">/usr/bin/java -cp /var/lib1.jar:/var/lib2.jar tool.MyApp  -n ${number} ${input} &gt; ${output}</command>
    <param format="vcf" name="input" type="data" label="Source VCF" optional="false"/>
    <param name="number" type="integer" value="10" label="Number of rows" optional="true"/>
    <data format="input" name="output" metadata_source="input"/>


1) the following xml raises an error in galaxy: (why)

/usr/bin/java  : cannot execute binary file

2) where can I find the documentation about defining a global variable/parameter to replace :




3) if I fix an error in my tool.xml, do I have to restart my instance of galaxy ?

4) are XML-inclusions (x:include) supported by the XML processing of tools.xml ?

Thank you



tool java custom • 2.0k views
ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by plindenbaum90
gravatar for Bjoern Gruening
3.9 years ago by
Bjoern Gruening5.0k
Bjoern Gruening5.0k wrote:

Hi Pierre,

I do not know why 1) is happening for you but

<command>java -cp /var/... </command>

should work.

2) setting the classpath and with that defining a tool dependency can be done with a tool_dependencies.xml file and the Galaxy Tool Shed. The resulting command will look like that.

<command> java -cp \$MY_JAR_PATH/myjava.jar </command>

Defining tool dependencies can be very elaborated and I would recommend to stick with full paths at the beginning and if you are happy with your tool, dive into the Galaxy Tool Shed. It's worth it!

3) If you have made changes to your tool, you need to reload the tool. That can be done either by restarting Galaxy, or reloading your tool via the Admin Panel. The latter is very convenient for development.

If you like have a look at galaxytools, it is a collection of a variety of different Galaxy tools with Tool Shed integration. You will also find Java examples, like GATK, SNPEff or minced, with a different level of complexity.

Have fun and enjoy Galaxy!



ADD COMMENTlink written 3.9 years ago by Bjoern Gruening5.0k

FWIW: 1 is happening, because the interpreter value is prepended to command content, so what you are seeing is:

$ bash /usr/bin/java
/usr/bin/java: /usr/bin/java: cannot execute binary file

ADD REPLYlink written 3.9 years ago by Daniel Blankenberg ♦♦ 1.7k

I see ! thanks, I'll try tomorrow morning !

ADD REPLYlink written 3.9 years ago by plindenbaum90

should I wrap my java in a *.bash file or removing the @interpreter="bash" will work ?

ADD REPLYlink written 3.9 years ago by plindenbaum90

Removing the interpreter will work. Alternatively, you could set the interpreter to java and then remove java from the command text. Historically, with java, people tend to just remove the interpreter bit.

ADD REPLYlink written 3.9 years ago by Daniel Blankenberg ♦♦ 1.7k
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