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Topic: when linux version of MS-DIAL will be released (Read 384 times) previous topic - next topic

when linux version of MS-DIAL will be released

Hi MS-DIAL group, when will linux version will be released? It will facilitate the analysis of the large dataset.
Or it there any solution to run it in a linux system?

Re: when linux version of MS-DIAL will be released

Reply #1
Hi shengguan,

Thank you for posting.
This is the MSDIAL development team.
Now we are preparing console application for Linux.
Could you evaluate this?
https://briefcase.riken.jp/public/ZS7gQA8mdEOAWDc
This is alpha version of msdial console application for Linux.
There is problem with the output file name, but it works.
Thanks.

Yuki

Re: when linux version of MS-DIAL will be released

Reply #2
Hi Yuki,
thank you for the alpha version.
I have a blank + 3 abf files, lcmsdda.
  • Win GUI MS-DIAL 4.36 works fine
  • Win console MS-DIAL 4.36 works only with tutorial param file. If I export the params from v4.36, it doesn't work.
  • Linux console alpha does not work. Log is pasted below.
.
Problems
  • Paths. It seems that linux app doesn't parse the paths correctly. I had to use absolute paths to run it and the output is in the root instead of the output folder. Also the file names contain path (see ls output below)
  • Blank - when I set a blank filtering, I can't set blank file. I assume this was not implemented yet.
  • MSPs - I can't upload my MSP. I assume only included libraries are supported now.
  • Params - I have to use a simple param file from the demo files or edit the full version exported from MS-DIAL. Most probably MSP and 'blank' definition problem.
Best regards,
Ondrej

Code: [Select]
./MsdialConsoleApp lcmsdda -i /home/ondrej/MsdialConsoleApp_linux-x64/data/ -o /home/ondrej/MsdialConsoleApp_linux-x64/out/ -m /home/ondrej/MsdialConsoleApp_linux-x64/data/Msdial-lcms-dda-Param.txt -p
Loading library files..
Start processing..
/home/ondrej/MsdialConsoleApp_linux-x64/data/blank.abf
Reading data...
end peak picking
Exporting deconvolution results...
Reading data...
Exporting peak list data: /home/ondrej/MsdialConsoleApp_linux-x64/out/\blank.msdial

Deconvoluted peak count: 2990

/home/ondrej/MsdialConsoleApp_linux-x64/data/blank.abf finished
/home/ondrej/MsdialConsoleApp_linux-x64/data/S1.abf
Reading data...
end peak picking
Exporting deconvolution results...
Reading data...
Exporting peak list data: /home/ondrej/MsdialConsoleApp_linux-x64/out/\S1.msdial

Deconvoluted peak count: 6477

/home/ondrej/MsdialConsoleApp_linux-x64/data/S1.abf finished
/home/ondrej/MsdialConsoleApp_linux-x64/data/S2.abf
Reading data...
end peak picking
Exporting deconvolution results...
Reading data...
Exporting peak list data: /home/ondrej/MsdialConsoleApp_linux-x64/out/\S2.msdial

Deconvoluted peak count: 6611

/home/ondrej/MsdialConsoleApp_linux-x64/data/S2.abf finished
/home/ondrej/MsdialConsoleApp_linux-x64/data/S3.abf
Reading data...
end peak picking
Exporting deconvolution results...
Reading data...
Exporting peak list data: /home/ondrej/MsdialConsoleApp_linux-x64/out/\S3.msdial

Deconvoluted peak count: 6525

/home/ondrej/MsdialConsoleApp_linux-x64/data/S3.abf finished
Joint aligner finished
Reading data...
0 finished
Reading data...
1 finished
Reading data...
2 finished
Reading data...
3 finished
Start finalization
Calculating basic properties
End finalization
Start aligned eic
End aligned eic
Gap filling finished
Finalization finished
Now saving the project to be used in MSDIAL GUI...

strange files
Code: [Select]
ls -alF
total 60548
drwxrwxr-x 2 ondrej ondrej     4096 říj 30 09:54  ./
drwxrwxr-x 4 ondrej ondrej    24576 říj 30 09:54  ../
-rw-rw-r-- 1 ondrej ondrej   738521 říj 30 09:54 '\AlignResult-20201030953.arf2'
-rw-rw-r-- 1 ondrej ondrej   374618 říj 30 09:54 '\AlignResult-20201030953.dcl'
-rw-rw-r-- 1 ondrej ondrej 19111850 říj 30 09:54 '\AlignResult-20201030953.EIC.aef'
-rw-rw-r-- 1 ondrej ondrej  6066618 srp 25 09:38  blank.abf
-rw-rw-r-- 1 ondrej ondrej     4704 zář 17 07:38  LIBneg_FAs.msp
-rw-rw-r-- 1 ondrej ondrej     1535 srp 21  2017  Msdial-lcms-dda-Param.txt
-rw-rw-r-- 1 ondrej ondrej  4819494 říj 30 09:54 '\project_2020_10_30_9_53_50_tmpFolder\peaklist_0.pll'
-rw-rw-r-- 1 ondrej ondrej  4929846 říj 30 09:54 '\project_2020_10_30_9_53_50_tmpFolder\peaklist_1.pll'
-rw-rw-r-- 1 ondrej ondrej  4917734 říj 30 09:54 '\project_2020_10_30_9_53_50_tmpFolder\peaklist_2.pll'
-rw-rw-r-- 1 ondrej ondrej  4923190 říj 30 09:54 '\project_2020_10_30_9_53_50_tmpFolder\peaklist_3.pll'
-rw-rw-r-- 1 ondrej ondrej     8745 říj 30 09:54  Project-20201030953.mtd2
-rw-rw-r-- 1 ondrej ondrej  5313579 srp 25 09:38  S1.abf
-rw-rw-r-- 1 ondrej ondrej  5509016 srp 25 09:38  S2.abf
-rw-rw-r-- 1 ondrej ondrej  5222554 srp 25 09:38  S3.abf

Re: when linux version of MS-DIAL will be released

Reply #3
In our lab we have created a VM running windows to overall this problem in Linux.
But I am glad to start trying this new version and let you know!
Thanks this is a great news!

Paolo

Re: when linux version of MS-DIAL will be released

Reply #4
The Linux version will be super useful, especially for large dataset and for pipeline automation. Would you be releasing the source codes and compilation instruction as well?

One of the feature we'd like to request for in the console app is the ability to supply the sample definition (sample order, groups, etc) in a file.

Thanks!
Wen
 

Re: when linux version of MS-DIAL will be released

Reply #5
Thank you for reply and sorry for late reply.

I fixed file path problems. Now MS-DIAL generate results correctly.
Please check this.https://briefcase.riken.jp/public/nSlEQAPmX4OAeNQ

I tested bellow environments and demo data.http://prime.psc.riken.jp/compms/msdial/download/demo/MsdialConsoleApp%20demo%20files.zip
  • CentOS Linux release 7.4.1708 (Core).
  • Windows 10 Pro, WSL Kali GNU/Linux 2020.2


And, I will answer your suggestions and problems.

  • Paths - it fixed. Please check in your environment.
  • MSPs - in my environment, I couldn't reproduce this problem. It may related to file path problem.

About blank and sample definition file, we also think that it's better to implement these requests for console version. But now we are developing new feature of MS-DIAL GUI version. So it takes time to implement them. Sorry.
Thanks,

Yuki.

Re: when linux version of MS-DIAL will be released

Reply #6
Hi Yuki,

Thank you for your kind reply! The MS-dial and its console app have been instrumental for our studies. We are very grateful for what you've provided for the community.

Is there a possibility we can contribute the to the development of the Linux version of the console apps? We'd love to put some time and resource on the app, and possible enhance it to support the sample grouping, ion mobility support, for example.  

Wen

Re: when linux version of MS-DIAL will be released

Reply #7
Hi Wen,

thanks for asking. One issue for sharing the source code for example in a git repository is the licensing manner with MS vendors. Especially, a critical source code for reading their raw data (agilent, sciex, and bruker) cannot be distributed unless you have a contract with them. Of course, we can reorganize the .net solution project without the source codes involved to the raw data retrieving. Then, I can send it to you. But one disadvantage is that you cannot retrieve our latest updates for the source codes..
(Therefore, I always put my source codes, which can be put in public space, when a paper is published. )

Please let me know if needed.
Thanks,

Hiroshi

Re: when linux version of MS-DIAL will be released

Reply #8
Hi Hiroshi,

Thanks so much for your reply! The concern about the vendor software is totally understandable.

We do have most of the instruments in our labs, so we should have the arrangement to use the vendor specific functionality. For data pipeline, we usually convert the raw files to mzML or IBF first. Thus the console app can start with these standard file formats, instead of the vendor files.

Looking forward to contribute as much as we can. Please contact me at wen.yu@astrazeneca.com for follow-up.

Wen

Re: when linux version of MS-DIAL will be released

Reply #9
Hi Wen,

thanks, we will contact you privately for this.
Thanks

Hiroshi