Compiling Dintor on Mac OS X is a bit complicated and deserves some more information presented in this document.

Prerequisites

Things get a lot easier, if there are some package managers around. We highly recommend the following:

fink or homebrew
perlbrew
cpanm in perlbrew

Installation of Perl packages

Most of the Perl programs can be installed with cpanm from perlbrew. We have tested Dintor on Perl 5.10 (long time ago), 5.14 (as of 2019) and 5.28 (as of 2019, too). For example, Class::InsideOut is installed with cpanm as follows:

cpanm install Class::InsideOut

Manual installation of some packages

Few packages cannot be installed via cpanm, either they are not available or cause problems during compilation. These are listed here.

IO::Socket::SSL

As of writing this (2019-01-31), Fink's openssl library did not allow flawless compilation of Net::SSLeay, which is one of IO::Socket::SSL's dependencies. cpanm has an experimental option for passing building arguments, –configure-args, as otherwise the library located in /sw is not found. This and switching to GCC5 allows compilation, forcing installation as one or two unit tests fail:

cpanm install --force IO::Socket::SSL  \
  --configure-args='CC="env MACOSX_DEPLOYMENT_TARGET=10.4 gcc-fsf-5"
                    INC="-I/sw/include"
            LDFLAGS="-L/sw/lib"
            LD="env MACOSX_DEPLOYMENT_TARGET=10.4 gcc-fsf-5 -L/sw/lib"'

Notice the MACOSX_DEPLOYMENT_TARGET=10.4, which tells OSX to build binaries compatible with 10.4 and higher. Perl 5.28 by default has this set to 10.3, it probably also works with the variable set to this value. This can be found by looking at the output of perl -V

Bio::DB::HTS

This Perl module needs htslib from SAMTools, see Compiling C programs for Ensembl API below for more information.

The linker command has an option -Wl,-rpath,/sw/lib, which is incompatible with Perl's MACOSX_DEPLOYMENT_TARGET=10.3. According to an error message of the compiler this option is available only for 10.5 and higher. Compiling with 10.5 as shown above gives binary compatibility issues with Perl and libraries during runtime. So my solution is to provide a crafted cc command that removes this option from the build process that is handled deeply in Perl:

Be sure you are using the right Perl version, perl –version
Unset the default compiler: unset CC

Create a bash script $HOME/cc and make it executable:

#!/bin/bash
new=$(sed -E 's/-Wl,-rpath,\/sw\/lib//' <<<"$@")
clang $new

Make it first in PATH shell environment variable: export PATH="$HOME:$PATH"
cpanm install –force Bio::DB::HTS

Again, we –force installation, as there were two issues with a memory reallocation that was not allocated before. This is indeed worrying, but the Dintor code passed all unit tests with this Perl code.

Tabix

Tabix is part of the SAMTools suite, and has been integrated there. Even though the source code is mainted actively, we did not find the necessary Tabix.pm Perl module. Therefore, we remain with the pretty old tabix tool from git, tabix.git. The following shows installation for Perl 5.28

perlbrew use 5.28
git clone https://github.com/samtools/tabix.git tabix-git
cd tabix-git
make all
cd perl
perl Makefile.PL PREFIX="$HOME/perl5/perlbrew/perls/perl-5.28.1"
make
make install

There are some warnings, but they can be ignored. Ultimately, the binary tabix-git/tabix must be copied to some directory in the search path.

Compiling C programs for Ensembl API

The Dintor website hosts all necessary Ensembl Perl APIs in a file, ensembl-api.tgz. It also includes instructions for compilation of the small C programs that do the linkage disequilibrium calculations, which need htslib installed on the system. Using Fink on Mac OS X, this is accomplished by

sudo fink install libhts2-dev libhts2-shlibs

and on Linux these packages are called libhts2 and libhts2-dev.