PeptideShaker v2.0.0-beta and SearchGUI-4.0.0-beta now available for testing!

[Harald Barsnes]

Hi all,

It has taken a lot longer than expected, but the beta versions of PeptideShaker and SearchGUI are now finally available for testing!

- http://genesis.ugent.be/maven2/eu/isas/peptideshaker/PeptideShaker/2.0.0-beta/PeptideShaker-2.0.0-beta.zip

- http://genesis.ugent.be/maven2/eu/isas/searchgui/SearchGUI/4.0.0-beta/SearchGUI-4.0.0-beta-windows.zip

- http://genesis.ugent.be/maven2/eu/isas/searchgui/SearchGUI/4.0.0-beta/SearchGUI-4.0.0-beta-mac_and_linux.tar.gz

A new version of Reporter (compatible with the new release of PeptideShaker) is also available:

- http://genesis.ugent.be/maven2/eu/isas/reporter/Reporter/0.8.0-beta/Reporter-0.8.0-beta.zip

Note that these versions are for testing purposes only and may not be identical to the final releases.

Also note that the new versions are not backwards compatible, i.e. you cannot open projects or parameter files from previous versions.

This is due to the major changes required to address some of the underlying issue with the previous versions, especially with regards to memory handling and the use of multiple threads.

The large amount of required code changes and improvements also means that the results will not be identical to previous releases. The results should however not be dramatically different.

For an overview of the changes, please see the release notes: https://github.com/compomics/peptide-shaker-2.0-issue-tracker/wiki/ReleaseNotes.

As indicated in the release notes, all of the command lines have been refactored. Please see the following wikis for details:

- https://github.com/compomics/peptide-shaker-2.0-issue-tracker/wiki/IdentificationParametersCLI

- https://github.com/compomics/peptide-shaker-2.0-issue-tracker/wiki/PeptideShakerCLI

- https://github.com/compomics/peptide-shaker-2.0-issue-tracker/wiki/SearchCLI

We believe that most of the existing issues in both PeptideShaker and SearchGUI have been solved with these beta versions. But there will most likely be new (hopefully minor) issues that have to be sorted before the official releases.

If you come across any issues with the beta versions, or have any questions or feedback, please use this separate issues tracker dedicated to the beta releases: https://github.com/compomics/peptide-shaker-2.0-issue-tracker/issues.

Thanks in advanced for testing the beta releases!

Best regards,

Harald and Marc

[René Zahedi]

That's great news!

Best. 

René 

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