Tomas, I have had been able to run a couple of data sets on this beta-version now. It seems to work quite well. The only issue that I ran into was that I had to recreate a new batch file and save it in this version. My old batch files would not load. This makes sense given all of the changes to the batch mode processing, but is there a way to make it backwards compatible so that one could still use their old, saved batch methods, only needing to change where the files for each process would be pulled from? Also, it may be a good idea to have an overall configuration option that would allow the user to select the same setting for the whole batch process. In this way, rather than having to go into each step to indicate you want it to use the files generated by the previous step it could just be a setting that can be applied to the entire process.
Thanks, Mike _________________________________________________________________________________________ Michael D. Williams Postdoctoral Research Associate University of Florida mtdwilli...@ufl.edu -----Original Message----- From: Tomas Pluskal [mailto:plus...@oist.jp] Sent: Thursday, May 07, 2015 7:37 PM 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=V >>>>> A_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 ------------------------------------------------------------------------------ One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
