#SEARCHGUI PROTEOMICS UPDATE#
#SEARCHGUI PROTEOMICS ZIP#

What do you think? If we add this, I’m thinking that it should just go straight in the PeptideShaker toolshed package because it is completely specialised on these tools. and another type called “peptideshakerzip”, it would also make workflows easier since galaxy could tell the difference between outputs from SearchGUI versus PeptideShaker?

If we defined a type called “searchguizip” (subtype of Binary). I’m not sure of all the subtleties … but at the very least these should have extension “zip” rather than “bgzip”.

#SEARCHGUI PROTEOMICS ZIP#

and this isn’t really appropriate since it looks like SearchGUI and PeptideShaker both create ZIP files. As far as I can tell Galaxy only has the type “bgzip”. In the first version of the Galaxy tool we can live with a little inefficiency (the database will need to be reindexed every time) … most Galaxy jobs tend to be run on pretty high end machines with heaps of memory, so hopefully it will be quick.ījoern, one thing I was wondering was whether we should define a new datatype for the zip files. I agree … let’s not worry about this for now. > backwards compatible command-line changes) to be aware of it would be > I haven't really kept up with changes since last time, but I'm > the commands you used in the new version. > version? If you used the command-line it would be very useful to know > Candace, did you use the command-line for your searches, or the GUI

> I am happy to work on this on Monday, if Bjoern has not already > Let me know if you need more information about any of these.

#SEARCHGUI PROTEOMICS UPDATE#

> - Added a new command line parameter called species_update to the PeptideShakerCLI to control the update of the species and GO mappings. > - Possible to set the number of threads used via -threads. > - Zip export from the command line (-zip). > - Possible to import zipped SearchGUI projects. > - The output can now zipped, see 'Optional output compression parameters' in the wiki. > - Renamed 'no enzyme' to the more understandable 'unspecific'. > - MS Amanda is now supported on Linux and Mac (requires Mono: ). > I had a quick look at the changes in SearchGUI and PeptideShaker compared to the versions currently in the toolshed. > On, at 12:37 am, Harald Barsnes wrote: and then to be able to download the results for use on the desktop app. From what I can remember, the idea was for the Galaxy tools to be able to run SearchGUI, and peptideshaker. I'm assuming Pratik and Candace would like the wrappers to make use of the new zipped output style.

Searchgui proteomics