#203 Bullseye does not follow spec

[William S Noble]

I just downloaded the Windows version of Bullseye and ran it on this RAW file:

/net/maccoss/vol9/raw_data/slu_Orbi2/Hoopmann/ASMS2008/051708-worm-ASMS-10.RAW

I used all default options and provided the RAW file twice on the command line (because it contains both MS1 and MS2 data). I noticed several problems:

(1) The program outputs two file, "hardklor.mono.txt" and "ISOTOPE.DAT" that are not documented.
(2) The stderr messages are not captured in the log file.
(3) The HTML spec is actually incomplete, because it says that we output the same format as the input. This doesn't make sense when the input is RAW. I think we actually default to outputting MS2.

I will begin by fixing the specification, and then hand this issue off to Kaipo.

[Kaipo]

Here is a patch to fix the second problem.
There are issues with outputting/overwriting the Hardklor/Bullseye progress percentages, so I only capture the cout from Hardklor/Bullseye, and changed the progress percentages to go to cerr instead of cout.

[William S Noble]

Ironically, I have no access to a Windows compiler, and no access to
non-RAW data. Can you either send me a Windows binary of Crux that
includes this patch, or else extract the MS1 and MS2 scans separately from
the RAW file that is referenced in this issue?

Thanks.
Bill

On Mon, Oct 13, 2014 at 2:17 PM, Kaipo kaipot@users.sf.net wrote:

Here is a patch to fix the second problem.
There are issues with outputting/overwriting the Hardklor/Bullseye
progress percentages, so I only capture the cout from Hardklor/Bullseye,
and changed the progress percentages to go to cerr instead of cout.

Attachment: bullseye-cout.diff (5.5 kB; text/x-patch)

• [issues:#203] http://sourceforge.net/p/cruxtoolkit/issues/203 Bullseye
  does not follow spec*

Status: open
Milestone: post v2.0
Labels: High priority
Created: Mon Oct 13, 2014 07:28 PM UTC by William S Noble
Last Updated: Mon Oct 13, 2014 07:28 PM UTC
Owner: William S Noble

I just downloaded the Windows version of Bullseye and ran it on this RAW
file:

/net/maccoss/vol9/raw_data/slu_Orbi2/Hoopmann/ASMS2008/051708-worm-ASMS-10.RAW

I used all default options and provided the RAW file twice on the command
line (because it contains both MS1 and MS2 data). I noticed several
problems:

(1) The program outputs two file, "hardklor.mono.txt" and "ISOTOPE.DAT"
that are not documented.
(2) The stderr messages are not captured in the log file.
(3) The HTML spec is actually incomplete, because it says that we output
the same format as the input. This doesn't make sense when the input is
RAW. I think we actually default to outputting MS2.

I will begin by fixing the specification, and then hand this issue off to
Kaipo.

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[Kaipo]

Charles, would you mind compiling a binary with this patch while I figure out this missing dll issue on my computer?

[Charles E. Grant]

Hi Kaipo,

On Oct 20, 2014, at 10:17 AM, Kaipo kaipot@users.sf.net wrote:

Charles, would you mind compiling a binary with this patch while I figure out this missing dll issue on my computer?

I'm building it now.

Charles

[Charles E. Grant]

Hi Kaipo,

On Oct 20, 2014, at 10:17 AM, Kaipo kaipot@users.sf.net wrote:

Charles, would you mind compiling a binary with this patch while I figure out this missing dll issue on my computer?

The Crux trunk doesn't compile currently because of Pwiz problems with the Shimadzu reader. I'm trying to build now with the patch applied to the crux-2.1 tag.

Charles