Hi Adam,
Try the Docker container here:
https://hub.docker.com/r/chambm/pwiz-skyline-i-agree-to-the-vendor-licenses/
Use the "x64" tag.
It uses Wine to run the Windows version of msconvert. It works for most vendor
formats:
https://github.com/phnmnl/container-pwiz/issues/8#issuecomment-408958177
-Matt
On 9/9/2018 2:39 PM, Adam Rabalski wrote:
Never got a reply directly back but the post was answered on the sourceforge
site:
https://sourceforge.net/p/proteowizard/mailman/message/36379927/
Short answer is no long answer is it would take a rewrite to implement on linux.
On Monday, August 20, 2018 at 10:03:37 PM UTC-5, Adam Rabalski wrote:
Never received a response back from the folks at ProteoWizard. If anyone
else has learned of anything new, please share!
On Monday, July 30, 2018 at 8:54:34 PM UTC-5, Adam Rabalski wrote:
Hi Mike,
Thanks for the clarification. I've sent the folks at ProteoWizard an
e-mail. Anything I learn I'll post in the forum.
Best,
Adam
On Monday, July 30, 2018 at 7:10:23 PM UTC-5, Michael Hoopmann wrote:
Hi Adam,
Yes, that is the linux compatible driver. Specifically, it works
through Mono. However, I'm not sure if any existing
converters have been updated to make use of it. msconvert is
maintained by ProteoWizard, and it might be best to see if they
have a linux version that uses those drivers. I am not sure what VM
we use for our msconvert via linux, but perhaps someone
else on this board knows.
Cheers,
Mike
On Monday, July 30, 2018 at 12:54:45 PM UTC-7, Adam Rabalski wrote:
Hi Mike,
Do you know if this has changed recently? I see that Thermo has
a RawFileReader that they say is compatible with linux now
http://planetorbitrap.com/rawfilereader#.W19raqdKi71
<http://planetorbitrap.com/rawfilereader#.W19raqdKi71> Is this the
linux compatible driver you speak of? Is there a msconvert
version that can take the vendor library from thermo and
convert raw -> mzML in linux? Or is this still only possible
through mono or a windows vm? How does your group at ISB
handle this and which VM setup do you recommend?
Best,
Adam
On Saturday, June 2, 2018 at 11:06:48 AM UTC-5, Michael
Hoopmann wrote:
No, there isn't a native tool for Linux that reads vendor
formats. Unfortunately, vendor formats are proprietary and
requires the vendor drivers to access those files and
convert them. All of those drivers are Windows only, as the
vendors have decided that is their platform of choice.
Thermo will eventually release a Linux compatible driver set
for Mono, maybe you can even get your hands on the
development version - but it will only read the file. Converting it
to another format will require additional coding or
interfacing with ProteoWizard.
One possible solution would be to create a Windows virtual
machine for converting vendor formats. It can be fired up
inside Linux, then convert the vendor files to mzML using
msconvert from ProteoWizard, copy the mzML files back to
your Linux filesystem, and wind down the VM.
Cheers,
Mike
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