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KNIME is a modular data exploration platform that enables the user to visually create data flows (often referred to as pipelines), selectively execute some or all analysis steps, and later investigate the results through interactive views on data and models.

Availability: 

All managed Linux workstations and managed Windows workstations.

The version on CMI managed Linux workstations contains the non-free Schrodinger workflows.

Instructions for users: 

On Linux

 $ module add knime 
 $ knime 

On Windows the package may already be installed on your machine if you're in the CMI. If not, ask the Computer Officers to add it to the list of automatically installed software for your machine.

Licence Details: 

KNIME has a dual licence scheme. For the CMI copy we are using the non-Free version so this software is not available outside the CMI. Please see https://www.knime.com/ and our KNIME page for licence details.

Admin notes: 

KNIME itself is very easy to install. Just unpack it into where you want it to go, usually a copy in /usr/local/ucc/knime/version and one in /usr/local/shared/knime/version. Once you've done that, install extensions. Run it as root and go to File, Install KNIME extensions. Install everything you can get your hands on. On Trusty we need to install an older Webkit which we can get through this interface in order for the builtin KNIME help browser to work, but to find it it's necessary to untick 'Group items by category' and then search for 'xul'. Just doing 'select all' doesn't seem to cause this one to get installed.

We also install the Schrodinger extensions into the ucc version. This makes our KNIME non-free. This can be done from the GUI extsion installer by pointing it at https://support.schrodinger.com/releases/knime/extensions/ and entering someone's Schrodinger account details; it can then download the extensions.

An install without the GUI can be done like this

export PATH=/usr/local/ucc/knime/whatever:$PATH  
  export PATH=$PATH:/usr/local/ucc/schrodinger/whatever  
  export SCHRODINGER=/usr/local/ucc/schrodinger/whatever  
  export LD_LIBRARY_PATH=/usr/local/ucc/schrodinger/whatever/mmshare-whatever/lib/Linux-x86_64  
  export SCHROD_LICENSE_FILE=/usr/local/ucc/schrodinger/current/license  
  export MMSHARE=/usr/local/ucc/schrodinger/whatever/mmshare-whatever/lib/Linux-x86_64    
  export MMSHARE_EXEC=/usr/local/ucc/schrodinger/whatever/mmshare-whatever/bin/Linux-x86_64  
        
  1. Install the latest Schrodinger.
  2. Set up the environment, replacing the whatevers with the appropriate versions for your Schrodinger and KNIME versions
  3. Get hold of the Schrodinger updatesite file for your Schrodinger version. That's not the same thing as the Schrodinger workflows file you download with Schrodinger. I got a copy from https://support.schrodinger.com/releases/knime/zippedUpdateSite/.
  4. Run "$SCHRODINGER/run" -verbose -FROM knime KNIME_install.py -install_basechem 2.9 /usr/local/ucc/knime/2.9.4/ but replace version numbers as needed.
  5. Run "$SCHRODINGER/run" -FROM knime KNIME_install.py -schrod_updatesite /scratch/SchrodingerKNIMEUpdateSite_2014-2.zip /usr/local/ucc/knime/whatever

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