blend4j - Running a galaxy tool ?

Question: blend4j - Running a galaxy tool ?

4.1 years ago by

Germany

Hi all,

How can I run a galaxy tool by using the blend4j package (http://jmchilton.github.io/blend4j/apidocs/) ?

I have successfully managed to do it from Python command line (http://bioblend.readthedocs.org/en/latest/api_docs/galaxy/all.html) by using the following command:
toolClient.run_tool(history_id=history['id'], tool_id=TOOL_ID, tool_inputs=params)

However I have not identified any corresponding method in com.github.jmchilton.blend4j.galaxy.ToolsClient (http://jmchilton.github.io/blend4j/apidocs/com/github/jmchilton/blend4j/galaxy/ToolsClient.html).

I am pretty sure this functionality is somewhere in the blend4j package.

Thanks,
Erno Lindfors

blend4j galaxy • 881 views

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modified 4.1 years ago • written 4.1 years ago by lindfors.erno • 30

4.1 years ago by

jmchilton ♦ 1.1k

United States

jmchilton ♦ 1.1k wrote:

Blend4j is always lagging behind bioblend - it just doesn't have as many people actively using it. So the newest version of blend4j in Maven central has an incredibly limited ability to run tools - like it cannot even specify input files I don't think.

I have created a branch of blend4j with some improvements that allow a simple example of running a tool such as randomlines to work. If you want to checkout, compile, and install that branch a simple example call would be something like:

    final History history = TestHelpers.createTestHistoryObject(instance, "randomlineshistorytest");
    final String inputId = TestHelpers.populateTestDataset(instance, history.getId(), "1\n2\n3\n");

    final Map<String, Object> parameters = new HashMap<String, Object>();
    final Map<String, String> inputDict = new HashMap<String, String>();
    inputDict.put("src", "hda");
    inputDict.put("id", inputId);
    parameters.put("input", inputDict);
    parameters.put("num_lines", "1");
    final ToolInputs toolInputs = new ToolInputs("random_lines1", parameters);
    client.create(history, toolInputs);

It is pretty low-level to use and doesn't produce parsed result data structures, etc... so I am not sure it is terribly useful yet even with the changes in that branch. I have created an issue on Github to address these short-comings.

Sorry I don't have better news.

ADD COMMENT • link written 4.1 years ago by jmchilton ♦ 1.1k

4.1 years ago by

lindfors.erno • 30

Germany

lindfors.erno • 30 wrote:

Thanks again for your prompt help!
I have been looking into your improved blend4j package.
However as you anticipated I feel maybe it is a bit too unstable for my purpose, so I think for the moment I will just call python directly from Java (a bit dirty but should work), and perhaps will switch to blend4j when a more stable package is available.

Thanks,
Erno Lindfors

ADD COMMENT • link written 4.1 years ago by lindfors.erno • 30

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