SeqAn Preferences not working

SeqAn Preferences not working - "Find in Path" and "Find in directory" do not work; I'm not yet sufficiently familiar with SeqAn to know which apps should be used for each 'tool'.

I'm using Windows 7 64-bit with Knime 2.9.2 nightly build.

Any ideas?

Steve. 

He Steve,

could you please specify what you mean by '"Find in Path" and "Find in directory" do not work'? "Find Path" will most likely not work, if you don't have SeqAn installed and the executables in your PATH. With "Find directory" you can select a directory where the executables are located, but this again requires the executables to be available on your system.

For mac and linux we ship the binaries but for windows only parts of the binaries are available, i.e., SeqAn itself is available for windows, but part of NGS toolbox (shipped together with the SeqAn Nodes) are only partially available for Windows.

If you tell me which nodes you need I could check if I find the matching binaries.

Cheers

Stephan

SeqAn executables are installed and the install location is in the system path; whether I choose "Find in Path" or use "Find in Directory" and browse to the install directory, none of the SeqAn applications are "filled in".

At the moment we're not sure which nodes we might need; I'd expect our users to be able to select what they need - which could in principle be any or all of the SeqAn tools.

I was able to work out the correct tool for some of the nodes; not sure about these:

FxBamCoverage & FxFastqStats;

MasonFragSequencing, MasonGenome, MasonMaterializer; MasonSimulator & MasonVariator.

Cheers,

SOH.

 

 

He Steve,

which version of SeqAn did you install on the machines? I guess it is not the preference dialog that isn't working, but your SeqAn installation is missing the above listed binaries. The SeqAN KNIME package is build based on our stable branch.

I will check if I we can deploy the matching SeqAn binaries for windows as well. I will keep you up-to-date. 

Cheers
Stephan

The version I downloaded was "seqan-apps-1.4.1-Windows-i686.zip".

Cheers,

SOH.

He Steve,

sorry it took some time but as of today the windows binaries of the SeqAn nodes are shipped with the KNIME plugin. I'm not sure wether an update is enough or if you have to first uninstall and then reinstall the SeqAn nodes for KNIME/Eclipse to realise that there is now an additional fragment containing the binaries. 

I hope this solves your problem.

Cheers
Stephan

After the last update, I'm seeing a whole of error messages such as:

ERROR     RepositoryManager                  Node de.seqan.ngs_toolbox.knime.nodes.SamToBam.SamToBamNodeFactory' from plugin 'de.seqan.ngs_toolbox' could not be created: Can't load factory class for node: de.seqan.ngs_toolbox.knime.nodes.SamToBam.SamToBamNodeFactory The corresponding plugin bundle could not be activated!

(also for openms nodes)?

Cheers,

Steve.
 

 

He Steve,

thanks for reporting this. I just checked it and it looks like this is an error specific to updating from an existing seqan/openms version. I could reproduced it with an existing installation, a freshly downloaded KNIME works, which is why I didn't saw it earlier. Sorry! 

I will try to fix this issue ASAP and keep you up-to-date.

Cheers
Stephan

He Steve,

the problem should be fixed. Just update to the most recent version of the SeqAn/OpenMS nodes. 

Cheers,
Stephan

Yes, seems to have been fixed now.

Thanks,

Steve.