I was trying to build genometools on my Mac laptop accoring to the INSTALL instructions but with no success.
I used genometools a lot for validating and fixing gff3 files. We had gt installed on the institute clusters but I wished to have it also on my Mac laptop so I can also work offline. To install genometools it’s easy for Debian and Ubuntu users through apt-get install but for Mac I need to build according to their instructions in the INSTALL file:
Building GenomeTools on Mac OS X (>= 10.6): ------------------------------------------- Make sure the command line developer tools are installed: $ xcode-select --install With these installed, you are ready to build GenomeTools without AnnotationSketch support (cairo=no). To build GenomeTools with AnnotationSketch, you can use Homebrew (https://brew.sh) to install the necessary dependencies required for building: $ brew install caskroom/cask/brew-cask $ brew cask install xquartz $ brew install cairo $ brew install pango To start the build process, invoke make as stated above.
I tried to install dependencies using brew and still got an error after make:
src/annotationsketch/graphics_cairo.c:29:10: fatal error: 'pango/pangocairo.h' file not found
Then I tried make cairo=no and got another error:
Undefined symbols for architecture x86_64: "_gt_lua_open_annotationsketch", referenced from: _gt_lua_open_lib in libgenometools.a(gt_lua.o) ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [bin/gt] Error 1
It’s a bit frustrating and then I had a look at the Issue tracker on the github page. I found this: https://github.com/genometools/genometools/issues/847 and the user said:
Nevermind I see its brew install genome tools. I wish this was clarified in the readme.
Yes, the actual easy way to use brew install genometools I hope they had put this in the instructions tool!
Now I can use:
gt gff3validator INPUT.gff gt gff3 [-retainids] [-tidy yes] [-sort] [-addintrons] INPUT.gff -o OUTPUT.gff gt stat [-intronlengthdistri] INPUT.gff