![]() ![]()
Part of the ToolShed repo is also ok.Reports of biogenic methane (CH 4) synthesis associated with a range of organisms have steadily accumulated in the literature. The policy for datatypes is currently not clear, we can also try to add > 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 ENZYME DEFINITION ZIPand 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”. > Bjoern, one thing I was wondering was whether we should define a new datatype for the zip files. 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. > I agree … let’s not worry about this for now. 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. 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 ENZYME DEFINITION 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". SEARCHGUI ENZYME DEFINITION MAC> - 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: SEARCHGUI ENZYME DEFINITION DOWNLOADand 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. ![]()
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |