Still Wining

[sr320]

Going the conversion route I still am having wine issues.

steven@emu:~/bioinfo/020917$ for file in *.raw;     do     no_path=${file##*/};     no_ext=${no_path%.raw};     WINEPREFIX=~/.wine32 wine ReAdW.2016010.msfilereader.exe "$file" "$no_ext".mzXML;     done
wine: cannot find L"C:\\windows\\system32\\ReAdW.2016010.msfilereader.exe"
steven@emu:~/bioinfo/020917$ Application tried to create a window, but no driver could be loaded.
Make sure that your X server is running and that $DISPLAY is set correctly.
err:systray:initialize_systray Could not create tray window

and hangs...

[kubu4]

Try specifying full path to ReAdW.2016010.msfilereader.exe

[seanb80]

I updated the /etc/environment path to include everything. I believe after logging out of your user account and logging back in it should work.

Previously, I'd just been adding paths to individual user accounts, this should be global.

[sr320]

@kubu4 full path is?

@seanb80 exited, quit terminal, relogged in....

steven@emu:~/bioinfo/020917$ for file in *.raw;     do     no_path=${file##*/};     no_ext=${no_path%.raw};     WINEPREFIX=~/.wine32 wine ReAdW.2016010.msfilereader.exe "$file" "$no_ext".mzXML;     done
wine: cannot find L"C:\\windows\\system32\\ReAdW.2016010.msfilereader.exe"
steven@emu:~/bioinfo/020917$ Application tried to create a window, but no driver could be loaded.
Make sure that your X server is running and that $DISPLAY is set correctly.
err:systray:initialize_systray Could not create tray window

still hanging

[kubu4]

I don't know. Full path is wherever that program is saved. I've never used it, so can't provide any help on locating it.

[kubu4]

Found it! (I used: which ReAdW.2016010.msfilereader.exe). It's here: /home/shared/ReAdW/ReAdW.2016010.msfilereader.exe

[sr320]

no luck

steven@emu:~/bioinfo/020917$ for file in *.raw
>     do
>     no_path=${file##*/}
>     no_ext=${no_path%.raw}
>     WINEPREFIX=~/.wine32 wine /home/shared/ReAdW/ReAdW.2016010.msfilereader.exe "$file" "$no_ext".mzXML
>     done
err:module:import_dll Library mfc100.dll (which is needed by L"Z:\\home\\shared\\ReAdW\\ReAdW.2016010.msfilereader.exe") not found
err:module:LdrInitializeThunk Main exe initialization for L"Z:\\home\\shared\\ReAdW\\ReAdW.2016010.msfilereader.exe" failed, status c0000135
steven@emu:~/bioinfo/020917$ Application tried to create a window, but no driver could be loaded.
Make sure that your X server is running and that $DISPLAY is set correctly.
err:systray:initialize_systray Could not create tray window

[seanb80]

I think it's an SSH issue, but am not sure, looking at it now.

[kubu4]

To get rid of the display error messages, edit the /etc/ssh/sshd_config file so that X11 forwarding is yes. This needs to be done on your local computer (it's already set to yes on Emu). Be sure to uncomment the line, in that config file. You may need to restart Terminal for the change to take effect.

The other library stuff is the real issue, though...

[seanb80]

It's a permission issue apparently. Am working on fixing it now.

Learned a valuable lesson though, never run anything involved with wine as sudo! It sets the owner to things as root, and finding everything that's been set as such is difficult.

[seanb80]

I believe I have it working now. Am testing a file and will write something up on Genefish once I'm sure.

[seanb80]

Ok. I'm 99.9% sure it works. I just converted a file on Steven's Emu account, and it completed.

using the command WINEPREFIX=~/.wine32 ReAdW.2016010.msfilereader.exe sample.raw sample.mzXML

I'll write up an overview of what went wrong, and how to fix it in the future. I'm also going to look into if it's possible to create a shared wine environment that everyone can use, as opposed to re-creating the environment for each new user account.

[sr320]

Believe this works!

Lets have everyone else use srlab account so this does not have to be fixed for all..

I presume this also means I could use windows version of comet and not convert?

steven@emu:~/bioinfo/020917$ WINEPREFIX=~/.wine32 ReAdW.2016010.msfilereader.exe \
> 20161205_Sample_1.raw \
> test-SR.mzXML
Application tried to create a window, but no driver could be loaded.
Make sure that your X server is running and that $DISPLAY is set correctly.
err:systray:initialize_systray Could not create tray window
fixme:thread:GetThreadPreferredUILanguages 52, 0x33fafc, 0x33fc74 0x33fb04
fixme:heap:HeapSetInformation (nil) 1 (nil) 0
ReAdW 2016.1.0(build Jun 21 2016 11:13:06)
Xcalibur interface initialized (5).
(Thermo lib opened file 20161205_Sample_1.raw)
file version is 66, interface version is 2.0 or greater
file should contain scan numbers 1 through 109165
(got computer name: emu)
Calculating sha1-sum of mzXML
--done (mzXML sha1):8ff1de9bb5ca369cce98859a506c3d166b56076a

steven@emu:~/bioinfo/020917$ head test-SR.mzXML 
<?xml version="1.0" encoding="ISO-8859-1"?>
<mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_3.1"
 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
 xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_3.1 http://sashimi.sourceforge.net/schema_revision/mzXML_3.1/mzXML_idx_3.1.xsd" >
 <msRun scanCount="109165" startTime="PT0.0281661S" endTime="PT8399.64S" >
  <parentFile fileName="20161205_Sample_1.raw" fileType="RAWData" fileSha1="9959094e2ae1c93e0439425418921b9df1c80000" />
  <msInstrument>
   <msManufacturer category="msManufacturer" value="Thermo" />
   <msModel category="msModel" value="Orbitrap Fusion Lumos" />
   <msIonisation category="msIonisation" value="NSI" />

It appears the loop command @kubu4 has on the wiki does not work...

steven@emu:~/bioinfo/020917$ for file in *.raw
>     do
>     no_path=${file##*/}
>     no_ext=${no_path%.raw}
>     WINEPREFIX=~/.wine32 wine ReAdW.2016010.msfilereader.exe "$file" "$no_ext".mzXML
>     done
wine: cannot find L"C:\\windows\\system32\\ReAdW.2016010.msfilereader.exe"
steven@emu:~/bioinfo/020917$ Application tried to create a window, but no driver could be loaded.
Make sure that your X server is running and that $DISPLAY is set correctly.
err:systray:initialize_systray Could not create tray window

I am going cross our for now so others do not go down this path..

[seanb80]

Yes, you should be able to use the win32 version of Comet to skip the conversion step.

[sr320]

I think I am now... thanks!

[kubu4]

Whoa! Just realized that the difference with the "for loop" and the working "one-liner" is the inclusion of wine after WINEPREFIX=~/.wine32! Removing that wine from the for loop version makes it work.

Was that the issue all along? Having that extra wine in the code?

I've udpated the wiki with the functioning for loop code, although it might not be needed any more, since it appears that comet is working...

[seanb80]

Interesting. I just tested running things without the wine part, and they seem to work. Apparently the WINEPREFIX=~/.wine32 part is enough?