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Describes the installation/update steps & troubleshooting
Featured, Phase-Deploy
Updated Jul 5, 2010 by aborgabor

Installation instructions

This page describes how to install/update the plugin to an existing KNIME installation.

You may also want to check the dependencies page

This video shows the installation of KNIME, HCDC and HiTS (without the R, Rserve, cellHTS2 installs):

Prerequisites

You need an installed KNIME 2.1.x (or above) installed on your computer. You can find instructions on how to install it at this page. If you are using an internet connection with proxy, you may want to set the appropriate preferences at File/Preferences.../General/Network Connections tab. Please note you have to check Enable proxy authentication if you have to give user name and password for your proxy connection.

You may want to look at this presentation if you are in trouble: HiTS Start and Setup KNIME

Important: You have to install the KNIME Distant Matrix Feature from the KNIME labs before installing the 0.2.0 feature.

You might want to add (somewhere after -vmargs) the following line to your knime.ini, which will allow you to use all available functionality: -Dknime.expert.mode=true

You can install additional nodes from the introduction page, or from the Help menu.

You should consider to increase the memory available to KNIME: edit knime.ini and change the lines starting with -Xmx and -XX:MaxPermSize=. The numbers following them are memory amount. The m means megabyte. The -XX:MaxPermSize= option influence the memory available to plugin code, while the -Xmx influence the available maximal memory (to both data and program code).

Install

You have to add a new update site to your KNIME installation. This should be: http://hits.googlecode.com/svn/trunk/ie.tcd.imm.hits.update/ You can set it in the Help/Software Updates.../Find and Install.../Search for new features to install Next, New Remote Site... and you can set any name you remember for the Name: field, and the http://hits.googlecode.com/svn/trunk/ie.tcd.imm.hits.update/ URL for the URL: field.

After you have set the update site, you can select it and click on Finish. (Here you may be prompted to your proxy user and password.) Recommended list of features (after the added labs update site (http://labs.knime.org/update/2.1)):

NameVersion
HiTS 3rd party components feature0.5.0.200912041736
HiTS main feature0.5.4.201007052109
HiTS experimental features0.4.1.200912041736
HiTS imaging feature0.1.0.200912041736
HiTS interoperability feature0.0.4.200912311558
KNIME utilities0.2.2.200912041736

Accept the license. After every plugins are installed you selected, you will be asked to restart your KNIME. Please do that.

Installation is complete. You can check if you see a HiTS group in your Node Repository, and some preferences in File/Preferences.../KNIME/HiTS Preferences

Update

This is similar to the install process. The possible options are:

  1. update all nodes with compatible updates
  2. update just the HiTS nodes

For the first option go to Help/Software Updates.../Find and Install.../Search for updates of the currently installed features, than click Finish. (Here you may be prompted to your proxy user and password.) If you have selected service updates, you might have to select Help/Software Updates.../Find and Install.../Search for new features to install.

For the second option go to Help/Software Updates.../Find and Install.../Search for new features to install Next and select the HiTS site. Click on Finish. (Here you may be prompted to your proxy user and password.) If there are updates you will have an option to select them. (If there are no updates you will get a message: No updates to the currently installed feature(s) found, try again later. And you do not have to do anything.) You have to accept the licenses. And install the features. When you are asked to restart your KNIME, please do that, by answering Yes.

Troubleshooting

The HiTS nodes are not visible in Node Repository

This might be because the labs' Distance Matrix feature was not installed before the install of HiTS. You have to uninstall HiTS, install the Distance Matrix feature, then install HiTS. Sorry about the confusion.

The Dendrogram with Heatmap and Sort by Cluster nodes are not available

You have to enable the experimental nodes by adding -Dknime.expert.mode=true line to your knime.ini file (somewhare after the -vmargs line)

Network problems

If you have not set properly the proxy configuration in your KNIME installation, you will have an error like this when you try to update or install your plugins:

Network connection problems encountered during search.

In the Details there is a message like this:

Unable to access "http://hits.googlecode.com/svn/trunk/ie.tcd.imm.hits.update/".

Error parsing site stream. [Premature end of file.]

Premature end of file.

Error parsing site stream. [Premature end of file.]

Premature end of file.

(If you do not have internet connection online, you will get the same message.) In this case please set it up properly.

Installed/updated but not working

You experience no problem installing the HiTS version 0.2.0 feature (using KNIME based on eclipse 3.3) from the update site, but the HiTS nodes are not available.

This happens when you install HiTS version 0.2.0 before the KNIME labs' Distance Matrix Feature. In this case you have to uninstall HiTS (Help/Software Updates/Manage Configuration/ find HiTS main feature, right click and select Uninstall, restart KNIME), install the Distance Matrix Feature, install HiTS.

Permgen space

You see something like this in the log: Permgen space and the nodes does not work.

In this case you should increase the -XX:MaxPermSize= parameter in knime.ini.

Comment by kvja...@gmail.com, Jan 24, 2010

Hi Gabor,

The node looks very promising! However the installation can not be finished. The KNIME Install module gives an error message: "Cannot find a solution satisfying the following requirements ie.tcd.imm.hits.common [0.0.4.200912041736]."

What can be the solution?

Cheers, Janos

Comment by project member aborgabor, Jan 25, 2010

Hi Janos,

Could you tell me which parts do you want to install? Selecting these should work (with KNIME 2.1.1): HiTS 3rd party components feature - 0.5.0.200912041736 HiTS experimental features - 0.4.1.200912041736 HiTS imaging feature - 0.1.0.200912041736 HiTS interoperability feature - 0.5.1.200912311558 KNIME utilities - 0.2.2.200912041736

Comment by kvja...@gmail.com, Jan 25, 2010

Hi Gabor,

Thanks the fast reply! I was impressed by your "Plate Heatmap" video ( http://www.youtube.com/watch?v=qgdVhJBScZk ) and that is what I try to reproduce using my HCS score results.

I selected those 5 components that you suggested (skipped the "HiTS main feature" that earlier seemed to be a necessary one).

Now I got a different dependency error message:

Cannot complete the request. See the details. Unsatisfied dependency: [ie.tcd.imm.hits.common 0.0.4.200912041736] requiredCapability: java.package/javax.annotation.concurrent/0.0.0 Unsatisfied dependency: [ie.tcd.imm.hits.common 0.0.4.200912041736] requiredCapability: java.package/javax.annotation.meta/0.0.0 Unsatisfied dependency: [ie.tcd.imm.hits.common 0.0.4.200912041736] requiredCapability: java.package/edu.umd.cs.findbugs.annotations/0.0.0 Unsatisfied dependency: [ie.tcd.imm.hits.common 0.0.4.200912041736] requiredCapability: java.package/javax.annotation/0.0.0 Unsatisfied dependency: [ie.tcd.imm.hits.common 0.0.4.200912041736] requiredCapability: java.package/javax.annotation.concurrent/0.0.0 Unsatisfied dependency: [ie.tcd.imm.hits.common 0.0.4.200912041736] requiredCapability: java.package/edu.umd.cs.findbugs.annotations/0.0.0 Unsatisfied dependency: [ie.tcd.imm.hits.common 0.0.4.200912041736] requiredCapability: java.package/javax.annotation.meta/0.0.0 Unsatisfied dependency: [ie.tcd.imm.hits.common 0.0.4.200912041736] requiredCapability: java.package/javax.annotation/0.0.0 Unsatisfied dependency: [ie.tcd.imm.hits.knime.interop.feature.feature.group 0.0.4.200912041736] requiredCapability: org.eclipse.equinox.p2.iu/ie.tcd.imm.hits.common/[0.0.3,1.0.0) Unsatisfied dependency: [ie.tcd.imm.hits.knime.interop.feature.feature.group 0.0.4.200912041736] requiredCapability: org.eclipse.equinox.p2.iu/ie.tcd.imm.hits.common/[0.0.4.200912041736,0.0.4.200912041736] Unsatisfied dependency: [ie.tcd.imm.hits.image.feature.feature.group 0.1.0.200912041736] requiredCapability: org.eclipse.equinox.p2.iu/ie.tcd.imm.hits.common/[0.0.4.200912041736,0.0.4.200912041736] Unsatisfied dependency: [ie.tcd.imm.hits.image.feature.feature.group 0.1.0.200912041736] requiredCapability: org.eclipse.equinox.p2.iu/ie.tcd.imm.hits.common/[0.0.3,1.0.0) Unsatisfied dependency: [ie.tcd.imm.knime.util.feature.feature.group 0.2.2.200912041736] requiredCapability: org.eclipse.equinox.p2.iu/ie.tcd.imm.hits.common/[0.0.3,1.0.0) Unsatisfied dependency: [ie.tcd.imm.knime.util.feature.feature.group 0.2.2.200912041736] requiredCapability: org.eclipse.equinox.p2.iu/ie.tcd.imm.hits.common/[0.0.4.200912041736,0.0.4.200912041736] Unsatisfied dependency: [ie.tcd.imm.hits.exp.feature.feature.group 0.4.1.200912041736] requiredCapability: org.eclipse.equinox.p2.iu/ie.tcd.imm.hits.common/[0.0.3,1.0.0)

Wondering what else is missing...

We could switch to Hungarian but English is better because these experiences might be useful for your broader user community besides of the Carpathian basin :)

Thanks again and cheers, Janos

-- Kriston-Vizi Janos PhD

Imaging Informatics Group Bioinformatics Institute (BII) Agency for Science, Technology and Research (A*STAR)

30 Biopolis Street #07-01, Matrix Building, Singapore 138671

Comment by project member aborgabor, Jan 26, 2010

Hi Janos,

Sorry, I think I accidentally missed the HiTS main feature from the list. It should be selected too (although the experimental part should include it as a dependency). The error message should not happen if the 3rd party components feature is selected, maybe a configuration problem in the installation description. (I will try to include these information to this page, thank you very much for your tries to use install it.)

To use the Plate Heatmap it is enough to install the HiTS main feature. To convert your data to a proper form, you might want to look at this help page: http://hits.googlecode.com/svn/ie.tcd.imm.hits/trunk/ie.tcd.imm.hits/help/heatmap.xhtml (Input data section). Cheers, gabor

PS.: I think English is fine, but it might be better to use a different form of communication (users list) after the install.

Comment by kvja...@gmail.com, Jan 26, 2010

Hi Gabor,

Thanks the heatmap help page, it looks great!

I added the HiTS main feature to the list and strictly followed your dependency installation instructions ( https://code.google.com/p/hits/wiki/Dependencies ) but the same dependency problem persists: the "common" feature requires java.package/javax.annotation... which is not available.

I'm ready to switch to the users list, pls give me a link where is it.

Cheers, Janos

Comment by project member aborgabor, Jan 26, 2010

Hi Janos,

The users group adress is the following: http://groups.google.com/group/HiTSusers I have added a recommended list of features to the install page (practically everything from the HiTS main group and the only option from the KNIME utilities group.) Do you use a special KNIME? Or without the KNIME labs update site? Thanks, gabor PS.: I am afraid I missed something from my install description, but I do not know what. I did multiple installs without problems (and one or two with some problems, but yours is a different one).

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