PeptideShaker

[Candace Guerrero]

Hello All,

If you don't remember me, my name is Candace and I'm a post-doc in Tim Griffin's lab at UofM. Last week our GalaxyP team met to discuss some topics in which we had some questions for the GalaxyP people out there :). We would like to wrap and use a good version of PeptideShaker. However, we are having questions with the cps files we generate in galaxy not working in desktop version of PeptideShaker. Is there a possible way to make the absolute files paths that generate the report relative paths so that the desktop version could open the cps files?

I know the PeptideShake has a new output option for making a zip file output. So if we wrapped PeptideShaker (PS) and made one of the history outputs for PS to be the "zip folder" does this contain all the files needed to open the PS project up on a outside version of desktop? If this doesn't work, is there a way to make the cps file generated from PS and the files needed to open the project work on relative paths instead of direct paths?

Basically, we want GalaxyP to run PS give us a cps file and then use that to open up on the desktop PS for viewing. Is this possible?

Thank you and Happy Holidays!

Candace

[harald.barsnes]

 

Hi Candace,

 

When opening the PeptideShaker cps file PeptideShaker will try to locate the needed files automatically. If the files are not found at the provided location, PeptideShaker will also check the folder where the cps file located and for a sub folder called data. If the files are still not found the user can locate them manually.

 

However, if you want to share the whole project or open it on a different computer, that is what the zip export is for. The zip file contains the cps file and a folder called data with the FASTA and mgf files. In other words all you need to open the project. And this should be exactly what you want.

 

As to the request for relative paths, given that PeptideShaker looks for the files in the same folder as the cps file (and in the data sub folder), I'd think that covers the support for relative paths too?

 

Best regards,

Harald

[Marc Vaudel]

Hi Candace,

As Harald mentioned and as detailed in an earlier mail, we designed the zip export so that you can run SearchGUI and PeptideShaker independently in Galaxy, and open the results on your desktop computer. You can hence create your project on galaxy, then, just unzip the file and open it in PeptideShaker to visualize the project on your computer.

Best regards,

Marc

--
You received this message because you are subscribed to the Google Groups "Galaxy for Proteomics" group.
To post to this group, send email to gal...@umn.edu.
Visit this group at http://groups.google.com/a/umn.edu/group/galaxyp/.
To view this discussion on the web visit https://groups.google.com/a/umn.edu/d/msgid/galaxyp/f70df011-398b-4fe8-ad5a-fd2493831f20%40umn.edu.

To unsubscribe from this group and stop receiving emails from it, send an email to galaxyp+u...@umn.edu.