crux 1.35 cygwin version

Arie Baratt

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Aug 15, 2011, 6:44:22 PM8/15/11

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Hi,

I installed the cygwin version of crux 1.35 and proceeded to run a sample search
as described at http://noble.gs.washington.edu/proj/crux/search-tutorial.html
I changed the PATH as prescribed and used the files demo.ms2 and
small-yeast.fasta as suggested. The problem is, when I type

$ crux search-for-matches demo.ms2 small-yeast.fasta

nothing happens. No error messages, no dump files, no
output. I must be missing something simple. An advise
will be highly appreciated.

Arie

Charles Grant

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Aug 15, 2011, 9:22:36 PM8/15/11

to Arie Baratt, crux-...@googlegroups.com

Hi Arie,

I just wanted to let you know that we received your message, and we're looking into the problem. Using the current version of Cygwin I was able to duplicate your problem: crux fails, but doesn't provide any messages or warnings. I should have an answer for you tomorrow.

Thanks for letting us know about this problem!

Charles

Arie

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Aug 18, 2011, 2:35:49 PM8/18/11

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Hi Charles,

Did you have any luck fixing the issue? Thank you!

Arie

On Aug 15, 6:22 pm, Charles Grant <erniegr...@gmail.com> wrote:
> Hi Arie,
>
> On Aug 15, 2011, at 3:44 PM, Arie Baratt wrote:
>
>
>
> > I installed the cygwin version of crux 1.35 and proceeded to run a sample search

> > as described athttp://noble.gs.washington.edu/proj/crux/search-tutorial.html

Charles Grant

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Aug 18, 2011, 5:47:50 PM8/18/11

to Arie, crux-users

Hi Arie,

On Aug 18, 2011, at 11:35 AM, Arie wrote:

>
> Did you have any luck fixing the issue? Thank you!
>

I'm not sure why the binary distribution of Crux 1.35 for Cygwin is failing. When I run any of the Crux tools from that distribution on a current version of Cygwin (1.7.9), I get exactly the results you found: no warnings, no messages, and no output. It is clearly failing almost immediately. However, when I build a fresh copy from the Crux 1.35 source, everything seems to work just fine. We definitely tested the Crux 1.35 distribution on Cygwin before putting it up on the web site, so my only guess is that there have been changes to the runtime libraries for Cygwin that keep Crux from working.

I built and tested a binary distribution of Crux 1.36 for Cygwin 1.7.9 and that is now available on the Crux web site. Could you download and install this new release and see if that resolves the problem?

Thanks for reporting the problem, and our apologies for the inconvenience.

Charles

Arie

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Aug 18, 2011, 6:07:35 PM8/18/11

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Charles,

Yes, Crux 1.36 seems to work just fine with Cygwin, thank you very
much!
Do I understand correctly that with the version 1.36 I'll be able to
search for post-translational modifications?

Arie

Charles Grant

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Aug 19, 2011, 7:32:23 PM8/19/11

to Arie, crux-users

Hi Arie,

On Aug 18, 2011, at 3:07 PM, Arie wrote:

> Yes, Crux 1.36 seems to work just fine with Cygwin, thank you very
> much!

Excellent!

> Do I understand correctly that with the version 1.36 I'll be able to
> search for post-translational modifications?

Well, Crux has supported post-translational modifications since about 1.20. Support for post-translational modifications is a new feature for the new release of Tide, but unfortunately Tide is not currently available for Cygwin.