command line interface tools - knime · 2017-05-23 · command line interface tools luis de la...
TRANSCRIPT
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