spctools-discuss Google Group

Re: [spctools-discuss] Re: building on windows

2009-11-06T23:27:14Z

Just about everything links against tpplib, so yes, if that's not happy
nobody's happy. And tpplib depends on zlib, so...

I think you're better off looking forward than backward, though, and I'd say
go with trunk.

Re: building on windows

2009-11-06T22:39:11Z

I couldn't get 4.3 to work so I went back to 4.2 (because it was the
release used in the documentation's build example).
It definitely got better and the build was running for about 45
minutes but still no joy. I hope you've seen this one:

LIB : fatal error LNK1181: cannot open input file 'C:\sashimi

Re: [spctools-discuss] Re: building on windows

2009-11-06T19:05:59Z

Branch should be fine - trunk build system is being worked on so no surprise
to find a hiccup there.

Re: building on windows

2009-11-06T18:41:47Z

Hi Brian,
I am using branch 4-3. do you know the last release that working?
Thanks for your help.
Bill

Re: [spctools-discuss] building on windows

2009-11-06T18:16:33Z

Try a release build first - it handles the uncompressing stuff. Apparently
just an oversight on the debug side, I'm sure it will get fixed soon, but
this should get you rolling.

Re: [spctools-discuss] from mzML to mzXML

2009-11-06T17:11:32Z

Hi Silvia,
It's easy to convert from mzML to mzXML with msconvert:
[link]
[link]
-Matt

from mzML to mzXML

2009-11-06T12:25:19Z

I have an Applied Biosystems 4800 MALDI TOF TOF and I use an LC-MALDI
workflow. Applied Biosystems gave me a tool to convert all T2D files
from an LC-run in a mzML file. For every run I have one mzML
containing MS and MSMS information. The question is: Can I go back
from mzML to mzXML? The majority of software up to today uses mzXML

Re: [spctools-discuss] building on windows

2009-11-06T16:48:46Z

Bill,

The VC build is not officially maintained, only a handful of folks use it so
when it breaks it can be a while before anyone notices. Which is probably
what happened here - I'll try a totally clean build and see what's what.

Brian Pratt
Insilicos

building on windows

2009-11-06T15:58:50Z

I'm building tpp on windows with VS8. I checked out 4.3. I have a
couple questions.

1. I wanted to check out the trunk but I could only find win_lib in
the branches; where is win_lib for the trunk?
2. I assume I need to extract some of the external libs but I can't
find anything in the readme files. In extern I found:

zero ions matched using X!Tandem + kscore on ETD data

2009-11-05T22:40:12Z

Hello All,

I'm using the latest stable release of TPP (4.3.1) to search some
phospho ETD data.
I've modified my tandem input file for ETD:
scoring, x ions: no
scoring, y ions: no
scoring, z ions: yes
scoring, a ions: no
scoring, b ions: no
scoring, c ions: yes

residue, potential modification mass: 15.994915@M,57@C

Re: Compile on OS X 10.6 snow leopard

2009-11-05T14:56:13Z

no prob. Also one other note (that was not picked up in the diff file)
is that the PWIZ_LITTLE_ENDIAN was note able to be defined in pwiz/
pwiz/utility/misc/endian.hpp, so just commented out the conditions to
set it. Didn't have time to trace how to set the proper flag to set
endianness uring the pwiz build, so you'll also need to account for

Importing Phenyx results

2009-11-05T14:21:49Z

Can anyone shed some light on how to get Phenyx results into the TPP?
I already have the pepxml output from Phenyx, but I imagine there is
some sort of conversion that needs to happen, as in its current state
the TPP doesnt seem to know what to do with it.

Thanks!

Chris

protxml2html.pl IProphet XSL Fix

2009-11-04T11:47:09Z

All,

I've previously had problems getting iProphet .prot.xml to display
correctly when using xsltproc on Fedora Core 8 as the xslt processor.
Everything worked with Xalan but not xsltproc, and error messages
where confusing. I've now had a chance to debug the xsl, and the issue
is that an xsl:param tag is incorrectly positioned - it is not the

Re: [spctools-discuss] Compile on OS X 10.6 snow leopard

2009-11-02T20:57:57Z

Thank you, Angel.

By the way, I've also switched to MacPorts (vs Fink) for future TPP
development work, but haven't yet tested the TPP with 10.6 (I'm
waiting until 10.6.2 at least), so this is appreciated.

-Natalie

Compile on OS X 10.6 snow leopard

2009-11-02T20:32:24Z

I use MacPorts, not fink, so I had to change Makefile.incl directly.
In addition, you need to change the BOOST_BJAM_EXEC location to work
on snow leopard. One final note is that the CGI/Makefile has an
unsupported flag in one of the copy operations.

Here is how to compile from source in OS X 10.6: