Wrapping latest version of PeptideShaker for GalaxyP.

[Pratik Jagtap]

Hello Ira and Bjoern,

I am copying JJ and Bart on this so that they are on the same page / can provide inputs regarding where to deposit the latest wrapped version of SearchGUI and PeptideShaker.

Regards,

Pratik

Pratik Jagtap,

Managing Director,

Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108

Phone: 612-624-9275

On Fri, Oct 24, 2014 at 3:55 PM, Ira Cooke <irac...@gmail.com> wrote:

Hi Bjoern, 

Great to hear from you. My preference would be to keep this as a separate repository as this will keep the commit history sensible (ie not filled with commits to other IUC tools), and will also mean that we can have our own wiki etc on bitbucket or github.   

In order to do automated testing with travis .. and to keep things similar to the IUC repo maybe we should move to github though.  If we do that I am happy to host the “master” repo on my account.

Currently the repository situation is that the “Master” is;

https://bitbucket.org/BjoernGruening/peptideshaker

I have a fork at 

https://bitbucket.org/iracooke/peptideshaker

but my fork is in sync with Bjoerns.

Cheers

Ira

On 24 Oct 2014, at 10:26 pm, Björn Grüning <bjoern....@gmail.com> wrote:

Hi Ira,

Thanks for this info.  I agree that it would be good to go for frequent updates (to avoid stagnation of the wrapper) … but the main issue is that with such frequent updates it’s often not feasible to thoroughly check the tool in between releases.  It’s quite easy for a small change in the CLI to break the wrapper.  Ideally we’d setup some automated testing for the wrapper .. (perhaps using planemo https://github.com/galaxyproject/planemo <https://github.com/galaxyproject/planemo> ) to ensure that our releases are not causing breakages.

I think Bjorn already has some experience with Planemo … what do you think about this Bjoern?  

Yes, this makes such stuff easier to setup. The current plan is to
integrate automatic testing and upload to the TS on the IUC repo. From
this we can take ideas and code to enable this also for the
peptide-shaker repository, or we just put it under IUC.

Comments welcome!

I really think we have a good Peptide Shaker wrapper. We need to split
the one wrapper into two ... and update the features. I don't think it
is much work, but I would like to have all different branches merged
that are floating around until I start to work on it again.

Cheers,
Bjoern

Cheers
Ira

On 24 Oct 2014, at 7:57 am, harald.barsnes <harald....@gmail.com> wrote:


Hi Pratik,

PeptideShaker v0.35.0 and SearchGUI v1.22.0 have just been released! So I'd recommend going with these latest versions. :)

Among the updates in the latest versions:
- Support for Comet (http://comet-ms.sourceforge.net <http://comet-ms.sourceforge.net/>). (Windows and Linux)
- Updated version of MS Amanda which now also is supported on Linux.*
- Complex PTM setups are now handled better.
- The processing of data in PeptideShaker is faster.

* At least in theory. It requires the installation of Mono (http://www.mono-project.com <http://www.mono-project.com/>), and should be regarded as beta. But might be worth a shot, as the results from our testing so far look pretty good.

As to the question of how often to update the SearchGUI and PeptideShaker versions in Galaxy, I'd say that once or twice a year sounds very infrequent. As you can see from our release notes we release new versions of our tools almost every month. Granted some of these are just minor updates and not all versions have to be wrapped for Galaxy. But if we wait half a year between each update then the versions in Galaxy will become fairly outdated compared to the standalone versions.

However, updating to new versions of SearchGUI and PeptideShaker should usually not require any change to the command lines, and should in most cases be as easy as replacing the two jar files? So unless the rest of the job of wrapping SearchGUI and PeptideShaker is very time consuming I don't see why more frequent updates should be a problem?

Best regards,
Harald




On Thursday, October 23, 2014 10:17:26 PM UTC+2, Pratik Jagtap wrote:
Hello Marc and Harald,

Great News !

While Candace is looking into 0.34 version outside of GalaxyP - we can discuss on plans to wrap the latest version of GalaxyP.

Harald and Marc - when do you anticipate 0.35 version to be available? Would it be worthwhile to wait for the new version and wrap for GalaxyP usage or do you think proceeding with 0.34 would be okay?

Ira and Bjoern - would you be able to wrap the latest version of  PeptideShaker (0.34 or 0.35 when it is available) - so that it can be uploaded onto the new GalaxyP instance?

Another decision we will have to make is on how frequently should PeptideShaker be Galaxy-wrapped? With frequent changes taking place we should make a decision on wrapping it once or twice a year. Any thoughts?

Looking forward to this project progressing further.

Regards,

Pratik

On Tue, Oct 21, 2014 at 4:13 AM, Marc Vaudel <mva...@gmail.com <javascript:>> wrote:
oops, sorry did not see that Harald already answered :)

2014-10-21 1:23 GMT+02:00 harald.barsnes <harald....@gmail.com <javascript:>>:

Hi Candace,

Ira is perfectly correct. In recent versions of PeptideShaker (starting from version 0.32.0) it is now possible to get all the required files in a single zip file by adding "-zip path_to_zip_file" to the PeptideShaker command line.

The created zip file will contain the PeptideShaker cps file and a data folder with the required fasta and mgf files.

As to the references to absolute paths, PeptideShaker will also look for the files in the same folder as the cps file and in any folders called "data". Or the user can provide missing files manually.

Best regards,
Harald
(Sorry if this message appears more than once. I first tried to reply directly to the e-mail.)



On Tuesday, October 21, 2014 12:47:23 AM UTC+2, iracooke wrote:
Hi Candace

It's great news that you are working on this!! I believe that recent versions of peptide shaker and searchgui have implemented a feature whereby all necessary files are packaged into a zip. I haven't explored this at all myself though so I can't say much about the details.

Best wishes

Ira


Sent from my iPhone

On 21 Oct 2014, at 7:31 am, Candace Guerrero <cgue...@umn.edu <>> wrote:

Hello Everyone,

Let me introduce myself. I am Candace - a new post-doc in Tim's lab and I will be working on testing of PeptideShaker tool witin GalaxyP.


I would like to give a short update for the PeptideShaker tool in GalaxyP 2014 (the latest version of GalaxyP).  Currently, PeptideShaker can successfully use a single file or data set collection to generate all PeptideShaker output options. However, when trying to open the cps file in a desktop version of PeptideShaker it fails to open. We believe this is due to the inability for PeptideShaker to access other files needed and that would usually be stored in the same path. Because cps files are storing absolute paths, there is no way for the desktop viewer to access these files when using GalaxyP 2014. Is there a way to package all the needed files in to a large comprehensive Galaxy cps file so that a desktop version of Peptide Shaker could open it?



Regards,



Candace


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