Running PIA via KNIME

Julian Uszkoreit edited this page Nov 8, 2018 · 29 revisions

Running PIA via KNIME is the recommended way for using PIA. It may be not as comfortable as running the web interface, but has some advantages when you need to apply the same steps to a number of PIA compilations or want to run a once set up workflow again and again. The downside of this is, that you need to run KNIME and PIA on a desktop computer or workstation instead of a (more powerful) server.

PIA is tested to run with at least KNIME 3.5.2.

Setup

After installing KNIME, start up the analystics platform and install the PIA nodes from the community contributions repository. For this, go to Help > Install New Software.... Select the community contributions repository under the Work with drop down menu, it should contain an address similar to http://update.knime.org/community-contributions/trusted/3.6. The PIA nodes can be found in the Bioinformatics & NGS group or simply by searching for them. Select the PIA nodes, click next, accept the license and restart KNIME after the installation is finished.

If all went well, you will see the PIA octopus on the splash screen of KNIME (together with all the other icons) and you will find the PIA nodes inside the Community Nodes in the Node Repository (usually left bottom side of screen).

PIA is in some parts demanding if it comes to main memory. You should at least allow KNIME to use 4GB, if possible even more (8GB to 16GB is necessary when merging many or large files) RAM. Please see here how to increase KNIME's allowed heap space.

Running PIA

All further information on how to run a PIA analysis can be found in the PIA tutorial: https://github.com/mpc-bioinformatics/pia-knime-nodes

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