Comments (6)
When I want to build MSConvert and SeeMS, the target that I tell quickbuild.bat to build is "executables".
The commandline I use is:
quickbuild.bat --i-agree-to-the-vendor-licenses -j2 toolset=msvc-14.3 address-model=64 --without-compassxtract executables
My machine is configured to be able to build Skyline, and there was no additional setup required to build MSConvert and SeeMS.
If you are still having trouble building you should attach your build output and we may be able to figure out what is going wrong.
from pwiz.
The MSConvertGUI build from Visual Studio should work after you've built using quickbuild.bat from the command-line. Make sure the VS config (release/debug) matches the quickbuild configuration (which defaults to release). You probably want the --i-agree* argument if you want vendor support, but it's not strictly required like it is for Skyline. Any C++ changes will require rebuilding with quickbuild.bat. Changes to the MSConvert or SeeMS C# code can be rebuilt/debugged from Visual Studio.
from pwiz.
Thanks @nickshulman and @chambm,
Following your suggestions, I did a fresh installation, cloned the repo, and ran the above command.
Build was still failing due to CustomDataSourceDialog import error, so after investigation I changed the pwiz_tools/MSConvertGUI/CustomDataSourceDialog/CustomDataSourceDialog.csproj file from
<TargetFrameworkVersion>v4.0</TargetFrameworkVersion>
to
<TargetFrameworkVersion>4.7.2</TargetFrameworkVersion>
and it worked in the release mode.
I want to execute the project in the bebug mode. Actually, I want to capture the input-output of the OverlapDemultiplexer that is defined in the Skyline. Also, when I import Skyline in MSConvert then it doesn't works. Any suggestions on it would be helpful.
from pwiz.
We recommend that you avoid the class "OverlapDemultiplexer" in Skyline.
That class was written before we understood the proper way to demultiplex overlapping isolation windows.
The demultiplexing that MSConvert does is much better than the thing that Skyline knows how to do.
That is, in the "Edit Isolation Scheme" dialog in Skyline, you should never choose anything other than "None" in the "Deconvolution" dropdown.
Instead, you should use MSConvert to generate demultiplexed .mzML files, and Skyline should not be told that the isolation windows ever overlapped.
from pwiz.
OK, thanks @nickshulman it was really helpful. One more thing, is there any way to plot the original multiplexed input and demultiplexed output generated by MSConvert. I checked SeeMS, but didn't found any option for it.
Thanks!
from pwiz.
The demultiplexing generates a different number of spectra, so it's tricky to directly compare them. But SeeMS will let you do it with a bit of work. The right click menu in SeeMS' spectrum list lets you overlay or stack spectrum graphs (on the current graph or a new tab). So if you view a spectrum in the original file, then go to the demultiplexed file and find the same spectrum (it will have the same "scan=XXX" number, there will be two versions (demux=0 and demux=1 IIRC). Select both demux=0 and demux=1 rows and right click, then select "Overlap on current graph" or "Stack on current graph".
from pwiz.
Related Issues (20)
- Could not automatically backport #2787
- Error/warning in converting .d Agilent file to mzML(vendor centroiding requested but not available for non-vendor formats...) HOT 1
- Bug: scan offset by +1 upon using the "--filter index" option HOT 1
- mzMLb. Handling of non-standard binary arrays. HOT 4
- O_RDWR vs. O_WRONLY HOT 9
- Thermo RawFileReader library is out-of-date HOT 5
- Unable to Locate 'titleMaker' Parameter in msconvert Options - Seeking Guidance
- old versions of pwiz matched in docker hub HOT 1
- Sciex Wiff2 files converted to MZML looses intensity HOT 1
- Permissions error extracting 7zz on Linux HOT 1
- Fails to build on Linux with missing librt HOT 2
- Pwiz build failed using GCC 13 on Linux
- High intensity TIC SeeMS compared to other softwares HOT 6
- ProteoWizard build issues under Windows 11 HOT 27
- Extraction of collision energy for Sciex 7600 scans in mzML format HOT 4
- Please fix Agilent .d derived mzML spectrum scan numbers to be sequential starting at 1 HOT 2
- "Consensus" representation of ETciD and EThcD spectra in MzML
- Could not automatically backport #3022 HOT 1
- Could not automatically backport #3023 HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from pwiz.