Mac install, Homebrew failing, make failing on lzma.h

[MartinPersida]

Hello,

I tried to install vt on Mac through homebrew and source and I ran into problem with both. According to the wiki documentation the classic use on mac is using homebrew as: brew install homebrew/science/vt However this results into the following message error: "Error: homebrew/science was deprecated. This tap is now empty as all its formulae were migrated." It seems that homebrew deleted the science branch and I didn't find the alternative one for vt. So cloned vt from github and run the makefile and got this error:

"cd lib/htslib; /Applications/Xcode.app/Contents/Developer/usr/bin/make libhts.a || exit 1; make[1]: ./version.sh: Command not found make[1]: ./version.sh: Command not found gcc -g -Wall -O2 -I. -c -o cram/cram_io.o cram/cram_io.c cram/cram_io.c:61:10: fatal error: 'lzma.h' file not found"

This is a similar problem which somehow has been raised previously and with other program installation on mac like samtools. So the problem come I think from the fact that I installed xcode with hombrew and that path is not in the include path (I try to add it in the makefile but without success). I solved it by copying lzma folder and .h directly into vt/lib/htslib. Is there something that should be done specificlly to install this lzma package before installing vt? It would be nice to have it mentionned in the installation paragraph of the wiki, as well as the new location of the homebrew branch for vt.

Regards

[atks]

@MartinPersida

Please pull down a new copy of vt. It should work now.

For the time being, we will still have to install the xz package via homebrew. I've updated the wiki to reflect that.

The htslib folks have solved this problem before but I am not sure why it has came back. It might be because of the new updates for OSX? I'm checking with them. https://github.com/samtools/htslib/pull/628

The science branch for homebrew has unfortunately been deprecated so I have no control over that. The person who set it up originally was another user.

[sbridel]

brew install Brewsci/science/vt nstead of brew install Homebrew/science/vt

and vt is finally magically installed and working

[tseemann]

brew install brewsci/bio/vt

is the correct way now.

[jmarshall]

To activate HTSlib's workaround for macOS not having lzma.h, you need to run the configure script. Does this vt build process run HTSlib's configure?

[atks]

@jmarshall yes. https://github.com/atks/vt/blob/master/Makefile#L154