KentUtils Installation Problem
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Entering edit mode
6 months ago
mglasena ▴ 40

I am trying to download the gff3ToGenePred application from: https://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/

When I try to run the program, I get the following error:

rsync -aP \
   rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/macOSX.x86_64/gff3ToGenePred ./

chmod +x gff3ToGenePred

./gff3ToGenePred

dyld: Library not loaded: /usr/local/opt/freetype/lib/libfreetype.6.dylib
     Referenced from: /Users/matt/informatics/gff3ToGenePred
     Reason: image not found
Abort trap: 6
kenutils gff3ToGenePred gff3 UCSC gff • 590 views
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Entering edit mode
6 months ago

Dynamically-compiled binaries suck!

Here are its dependencies, where it expects to find the libraries it needs:

% otool -L ./gff3ToGenePred 
./gff3ToGenePred:
    /usr/local/opt/freetype/lib/libfreetype.6.dylib (compatibility version 24.0.0, current version 24.2.0)
    /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1281.100.1)
    /usr/lib/libiconv.2.dylib (compatibility version 7.0.0, current version 7.0.0)
    /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 902.1.0)

Short of recompiling this from source as a static binary, you could install the Freetype library via Homebrew:

% brew install freetype

Once installed, you should be able to run the gff3ToGenePred tool. If not, you can check where freetype is installed via:

% brew --prefix freetype
/usr/local/opt/freetype
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Entering edit mode

It looks like it was installed to

/opt/homebrew/opt/freetype

I don't have the directory that it expects:

/usr/local/opt

I'm not sure what to do now.

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1
Entering edit mode

You could try manually adding a directory and soft link:

% sudo mkdir -p /usr/local/opt
% sudo ln -s /opt/homebrew/opt/freetype /usr/local/opt/freetype

It may be better to update your Homebrew installation and related packages, though that would take some time and may break other things you use. Perhaps try the above and see if that works for you.

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Entering edit mode

Gave the above a try and got the following error:

dyld: Library not loaded: /usr/local/opt/freetype/lib/libfreetype.6.dylib
  Referenced from: /Users/matt/informatics/gff3ToGenePred
  Reason: no suitable image found.  Did find:
    /usr/local/opt/freetype/lib/libfreetype.6.dylib: mach-o, but wrong architecture
    /usr/local/opt/freetype/lib/libfreetype.6.dylib: stat() failed with errno=1
    /opt/homebrew/Cellar/freetype/2.10.4/lib/libfreetype.6.dylib: mach-o, but wrong architecture
Abort trap: 6
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Entering edit mode
6 months ago
GenoMax 111k

My answer here: Install Kent Source Archive Binaries

For your program use ucsc-gff3togenepred

Binaries available at UCSC site are compiled for macOS Catalina and do not work on macOS Big Sur.

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0
Entering edit mode

This did the trick! Thank you!

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