Tomas,
Thanks a bunch! I will start using this version right away! I appreciate your
hard work on a fantastic piece of software.
Mike
Sent on the run...
-------- Original message --------
From: Tomas Pluskal
Date:05/07/2015 19:36 (GMT-05:00)
To: Developer discussion
Cc: Gauthier Boaglio , "Williams,Michael Thomas David"
Subject: Re: [Mzmine-devel] Problem with Batch Mode in 2.14.2
Hi Gauthier, Mike,
I performed the change as discussed. The user can now select one of the five
options when choosing raw data files or peak lists.
Since this is a big change that affects almost all modules of MZmine, I would
really appreciate if you guys could help me testing it - especially in the
batch mode.
You can download the beta version of MZmine 2.15 here:
https://www.dropbox.com/s/zhp2nf3vq99zbj3/MZmine-2.15-beta.zip?dl=0
Please let me know if you find any problems.
Tomas
> On Apr 19, 2015, at 21:02, Gauthier Boaglio <gauthier.boag...@gmail.com>
> wrote:
>
> Hi Tomas,
>
> It certainly would ;), but this also would mean struggling back with the
> old design. As far as I remember, you changed drastically the model to
> get rid of the error prone (from dev point of view) system allowing to
> register the files generated by a given step. I'am not sure what is in
> play here, but I suppose, since you suggest a "use files generated by
> the previous step (in batch mode)" option, that you figured out a way to
> keep a clean and simple global model, and have this feature restored in
> the mean time (again, the piece of discussion we had at the time you
> changed the model). I am not up to date with the actual current model.
> Anyway, the options you are listing below would clearly make me happy
> (as a user, at least)... And this is the most important (as a dev, we
> always can adjust). Sounds like I want to have my cake and eat it, here,
> isn't... it ;)?
>
> I'll checkout the current MZmine source code, and see how it looks like
> ASAP, this way I'll probably be in a more comfortable position to make
> pertinent comments ;).
>
> Cheers,
> Gauthier
>
>
> On 04/19/2015 04:54 AM, Tomas Pluskal wrote:
>> Hi Gauthier, Mike,
>>
>> I can imagine the file selector could have several options:
>>
>> * use all files
>> * use currently selected files (in the GUI)
>> * use files generated by the previous step (in batch mode)
>> * select files manually
>> * select files using name pattern
>>
>> Would that make you happy? :)
>>
>> Cheers,
>>
>> Tomas
>>
>>
>>
>>> On Apr 19, 2015, at 1:48 AM, Gauthier Boaglio <gauthier.boag...@gmail.com>
>>> wrote:
>>>
>>> Hi all,
>>>
>>> Sounds like something that went on the table earlier ;)
>>>
>>> https://sourceforge.net/p/mzmine/mailman/message/33158142/
>>>
>>> The old way / design (before 2.13) was handy from user point of view
>>> because each step was getting automatically the files generated by the
>>> previous step as input for the next step, but was also causing issues
>>> (more from link above).
>>>
>>> Well, don't know if a compromise could be found. As a matter of fact,
>>> setting wildcards filtering for each step is constraining, from user side...
>>>
>>> Best,
>>> Gauthier
>>>
>>>
>>> On 04/18/2015 04:31 AM, Tomas Pluskal wrote:
>>>> Hi Mike,
>>>>
>>>> In the selection component you can use wildcards (*) to specify the names
>>>> of raw data files that will be used.
>>>>
>>>> For example
>>>> * will use all files
>>>> *filtered will use all files with name ending with "filtered"
>>>>
>>>> And so on. This way you can "program" the batch mode to use exactly the
>>>> right files in each step.
>>>>
>>>> Thinking about that, we could probably add an extra option "Use the files
>>>> currently selected in the project window". That would be useful for the
>>>> first step of the batch. I'll take a look at it later.
>>>>
>>>> Best,
>>>>
>>>> Tomas
>>>>
>>>>
>>>>
>>>>> On Apr 18, 2015, at 1:28 AM, Williams,Michael Thomas David
>>>>> <mtdwilli...@ufl.edu> wrote:
>>>>>
>>>>> Hello,
>>>>>
>>>>> I am having trouble running batch mode analysis using v. 2.14.2 (newest).
>>>>> In older versions (2.12 specifically) we are able to select all of the
>>>>> imported files and run a batch mod on all files without selecting
>>>>> specific file names for each process in the batch.
>>>>>
>>>>> Is there a way to do something similar with the current version? As it is
>>>>> now I have to manually select the files for each step in the batch
>>>>> sequence. Which at first is only the raw files. It runs through the Mass
>>>>> detection, but because old lists are replaced by new ones (with new
>>>>> names) in each subsequent step we get an error and these then have to be
>>>>> run manually since the peak list names change with each step
>>>>> (chromatogram builder, deconvolution, isotopic grouper, join aligner,
>>>>> etc.). Can this be fixed so that the batch process will work? This tends
>>>>> to save us a lot of time without having to come back to run each process
>>>>> manually.
>>>>>
>>>>> Thanks,
>>>>> Mike
>>>>>
>>>>>
>>>>> Michael D. Williams
>>>>> Postdoctoral Research Associate
>>>>> University of Florida
>>>>> mtdwilli...@ufl.edu
>>>>> ------------------------------------------------------------------------------
>>>>> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
>>>>> Develop your own process in accordance with the BPMN 2 standard
>>>>> Learn Process modeling best practices with Bonita BPM through live
>>>>> exercises
>>>>> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual-
>>>>> event?utm_
>>>>> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF_______________________________________________
>>>>> Mzmine-devel mailing list
>>>>> Mzmine-devel@lists.sourceforge.net
>>>>> https://lists.sourceforge.net/lists/listinfo/mzmine-devel
>>>> ===============================================
>>>> Tomas Pluskal
>>>> G0 Cell Unit, Okinawa Institute of Science and Technology Graduate
>>>> University
>>>> 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
>>>> WWW: https://groups.oist.jp/g0
>>>> TEL: +81-98-966-8684
>>>> Fax: +81-98-966-2890
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
>>>> Develop your own process in accordance with the BPMN 2 standard
>>>> Learn Process modeling best practices with Bonita BPM through live
>>>> exercises
>>>> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
>>>> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF
>>>> _______________________________________________
>>>> Mzmine-devel mailing list
>>>> Mzmine-devel@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/mzmine-devel
>>>
>>> --
>>> Gauthier BOAGLIO
>>> CEFE - UMR 5175
>>> 1919 route de Mende
>>> F-34293 Montpellier cedex 5
>>>
>>> Tel: +33/0 4 67 61 32 15
>>> Fax: +33/0 4 67 61 33 36
>>>
>>> email: gauthier.boag...@cefe.cnrs.fr
>>> www:
>>> http://www.cefe.cnrs.fr/en/evolutionary-ecology-and-epidemiology/gauthier-boaglio
>>> http://www.evolepid.org/people.php?name=boaglio
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
>>> Develop your own process in accordance with the BPMN 2 standard
>>> Learn Process modeling best practices with Bonita BPM through live exercises
>>> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
>>> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF
>>> _______________________________________________
>>> Mzmine-devel mailing list
>>> Mzmine-devel@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/mzmine-devel
>> ===============================================
>> Tomas Pluskal
>> G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University
>> 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
>> WWW: https://groups.oist.jp/g0
>> TEL: +81-98-966-8684
>> Fax: +81-98-966-2890
>>
>
>
> --
> Gauthier BOAGLIO
> CEFE - UMR 5175
> 1919 route de Mende
> F-34293 Montpellier cedex 5
>
> Tel: +33/0 4 67 61 32 15
> Fax: +33/0 4 67 61 33 36
>
> email: gauthier.boag...@cefe.cnrs.fr
> www:
> http://www.cefe.cnrs.fr/en/evolutionary-ecology-and-epidemiology/gauthier-boaglio
> http://www.evolepid.org/people.php?name=boaglio
>
>
> ------------------------------------------------------------------------------
> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
> Develop your own process in accordance with the BPMN 2 standard
> Learn Process modeling best practices with Bonita BPM through live exercises
> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF
> _______________________________________________
> Mzmine-devel mailing list
> Mzmine-devel@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/mzmine-devel
===============================================
Tomas Pluskal
G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University
1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
WWW: https://groups.oist.jp/g0
TEL: +81-98-966-8684
Fax: +81-98-966-2890
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