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Old 11-06-2013, 11:11 AM   #1
godzilla07
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Location: Berkeley California

Join Date: Nov 2010
Posts: 17
Smile Trinity will not install properly on Mac OS X

I tried to compile trinity r2013_08_14 on Mac OS X 7.5 and I got the report below:
Performing Unit Tests of Build

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

JellyFish: has been Installed Properly
Inchworm: has been Installed Properly
Chrysalis Installation appears to have FAILED
QuantifyGraph Installation appears to have FAILED
GraphFromFasta Installation appears to have FAILED
ReadsToTranscripts Installation appears to have FAILED
fastool: has been Installed Properly
parafly: has been Installed Properly
slclust: has been Installed Properly
collectl: has been Installed Properly

I have Xcode Version 4.6 (4H127)
Do I need to update my Xcode or does the Makefile not properly install?
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Old 11-06-2013, 01:32 PM   #2
jimmybee
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Location: Adelaide, Australia

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Posts: 119
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Quote:
Originally Posted by godzilla07 View Post
I tried to compile trinity r2013_08_14 on Mac OS X 7.5 and I got the report below:
Performing Unit Tests of Build

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

JellyFish: has been Installed Properly
Inchworm: has been Installed Properly
Chrysalis Installation appears to have FAILED
QuantifyGraph Installation appears to have FAILED
GraphFromFasta Installation appears to have FAILED
ReadsToTranscripts Installation appears to have FAILED
fastool: has been Installed Properly
parafly: has been Installed Properly
slclust: has been Installed Properly
collectl: has been Installed Properly

I have Xcode Version 4.6 (4H127)
Do I need to update my Xcode or does the Makefile not properly install?
Are there dependencies for ReadsToTranscripts, GraphFromFasta, QuantifyGraph and Chrysalis Installation? That would suggest why some installed and those failed....
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Old 11-07-2013, 12:28 PM   #3
Wallysb01
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Location: San Francisco, CA

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Posts: 286
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I don't think you'll ever get Trinity to work on OSX, at least not without some major changes.

I think you also need to set ulimit to be infinate, which to do on OSX requires recompiling the kernal to allow it, if I remember right....
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Old 11-07-2013, 01:42 PM   #4
mcnelson.phd
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Quote:
Originally Posted by Wallysb01 View Post
I don't think you'll ever get Trinity to work on OSX, at least not without some major changes.

I think you also need to set ulimit to be infinate, which to do on OSX requires recompiling the kernal to allow it, if I remember right....
We run Trinity on our MacPro without problems, although I'll admit that it hasn't been updated for a while so it's not the current version (we're still using version 2012-06-08 since we don't run trinity that often on our Mac).

It is true that the stack limits can kill a Trinity run on OSX, but it won't prevent you from installing anything (or at least it didn't use to). When you do get it installed, you'll just need to run the following before running Trinity in order to increase the stack limit to the OSX limit, which in all of our uses has never caused any problems.

Code:
ulimit -s 65532
I actually modified the main Trinity.pl script to check if that limit was increased and die if it hasn't been to prevent it from being an issue. Unfortunately because of how the restrictions for OSX work, a process cannot increase the user limits to be greater than the parent process, so everything inherits the maximum limit of the kernel which is 65532.
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Old 11-07-2013, 01:59 PM   #5
Wallysb01
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Location: San Francisco, CA

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Quote:
Originally Posted by mcnelson.phd View Post
We run Trinity on our MacPro without problems, although I'll admit that it hasn't been updated for a while so it's not the current version (we're still using version 2012-06-08 since we don't run trinity that often on our Mac).
Yeah, I remember getting Trinity to install but always having it error out with the stack limits. I had linux computers available to me though, so I never really bothered to fix that stack limit check. Anyway, nice work around, someone else might have to try to see if it will take on the new version.
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