New releases: SearchGUI 4.0.0 and PeptideShaker 2.0.0

[Harald Barsnes]

Hi all,

We've finally released the new major updates of both SearchGUI and PeptideShaker!

Note that there are lots of fixes and improvements this time around, so please read the release notes carefully before starting to use the new versions:

SearchGUI: https://github.com/compomics/searchgui/wiki/ReleaseNotes

PeptideShaker: https://github.com/compomics/peptide-shaker/wiki/ReleaseNotes

Please take extra note regarding the changes to the parameter files. Most notably the path to the FASTA file has been moved outside of the parameter file to make it easier to reuse parameter files across different setups. For more details please see:

IdentificationParametersCLI: https://github.com/compomics/compomics-utilities/wiki/IdentificationParametersCLI

SearchGUI: https://github.com/compomics/searchgui/wiki/SearchCLI

PeptideShaker: https://github.com/compomics/peptide-shaker/wiki/PeptideShakerCLI

With these new versions we hope that most of the earlier issues should be resolved. But as we rewrote almost all of the code to do so, there will also most likely be new bugs we have not yet detected ourselves. So if you do come across any issues, please do not hesitate to let us know via the issue trackers:

SearchGUI: https://github.com/compomics/searchgui/issues

PeptideShaker: https://github.com/compomics/peptide-shaker/issues

Best regards,

Harald

[Harald Barsnes]

Hi again,

I forgot to mention that the new releases require Java 9 or newer. So if you're still using Java 8 this might be a good opportunity to update your Java version.

Also, note that given the structural changes to the parameter files, these have to be recreated for use in the releases, i.e. you cannot use your old parameter files.

And on a related note, the saved PeptideShaker project format has also changed (from .cpsx to .psdb) and the old files cannot be open in the new release. Basically the underlying database structure was completely rewritten in order to fix particularly nasty bugs. You can of course still open your old projects in the previous PeptideShaker releases if you need to.

Best regards,

Harald