Command line interface tools

2 Luis de la Garza GKN: Integrating command line tools into KNIME

as versatile as the Internet

Command line interface tools

3 Luis de la Garza GKN: Integrating command line tools into KNIME

together we stand, divided we fall

Command line interface tools

4 Luis de la Garza GKN: Integrating command line tools into KNIME

ain’t nobody got time for that!

40+ tools

170+ tools

60+ tools

ToolNodeModel.java

ToolNodeDialog.java

ToolNodeFactory.java

ToolNodeFactory.xml

Common tool descriptor

5 Luis de la Garza GKN: Integrating command line tools into KNIME

whatcha doin’?

input0

input1

output0

output1

output2

param0

Common tool descriptor

6 Luis de la Garza GKN: Integrating command line tools into KNIME

I see what you did there

<tool name="MagicSauce">

<ITEM name="i" type="input-file" value="in.pdb" />

<ITEM name="o" type="output-file" value="out.pdb"/>

<ITEM name="ph" type="float" value="7.2" />

<ITEM name="alg" type="string" value="greedy” />

</tool>

my_first_tool.ctd

Command line tool integration

7 Luis de la Garza GKN: Integrating command line tools into KNIME

KNIME: silent “K”, loud success

Command line tool integration

8 Luis de la Garza GKN: Integrating command line tools into KNIME

will it blend?

MagicSauce

Command line tool integration

9 Luis de la Garza GKN: Integrating command line tools into KNIME

yes we can!

Generic KNIME Nodes

node_generator

my_first_tool.ctd

MagicSauceNodeModel.java

MagicSauceNodeDialog.java

MagicSauceNodeFactory.java

MagicSauceNodeFactory.xml

Command line tool integration

10 Luis de la Garza GKN: Integrating command line tools into KNIME

I want more power!!!

Execution of distributed workflows

11 Luis de la Garza GKN: Integrating command line tools into KNIME

running almost anything almost anywhere

Execution of distributed workflows

12 Luis de la Garza GKN: Integrating command line tools into KNIME

stop, drop and roll instead of drag and drop

Side-to-side comparison

13 Luis de la Garza GKN: Integrating command line tools into KNIME

Free

distributed

execution

Intuitive GUI Smells good

✔ ✗ ✗

✗ ✔ ✗

✔ ✔ ✔

The challenge

14 Luis de la Garza GKN: Integrating command line tools into KNIME

any command line tool into KNIME,

any KNIME workflow on the cluster

Our vision: The best of both worlds

15 Luis de la Garza GKN: Integrating command line tools into KNIME

having your cake and eating it too

KNIME

Workflow Converter

design conversion execution

Acknowledgements

16 Luis de la Garza GKN: Integrating command line tools into KNIME

University of Tübingen

Oliver Kohlbacher

Freie Universität Berlin

Knut Reinert

University of Konstanz / KNIME.com

Thorsten Meinl

Bernd Wiswedel

Free agents (former members)

Stephan Aiche

Marc Röttig

Thanks

17 Luis de la Garza GKN: Integrating command line tools into KNIME

grateful speaker is grateful