#SAMTOOLS MACOS HOMEBREW HOW TO#
#SAMTOOLS MACOS HOMEBREW INSTALL#
#SAMTOOLS MACOS HOMEBREW MANUAL#
#SAMTOOLS MACOS HOMEBREW CODE#

Something along the lines of: curl -L | bash That might sound challenging but it is just a few commands.

#SAMTOOLS MACOS HOMEBREW INSTALL#

That would be my first step: set up perlbrew, install Perl 5.22, then install cpanminus. Other people may have their preferred method, but perlbrew (combined with cpanminus) will make this type of work fun and much less of a pain (and they are popular choices). You find it easier to manage Perl without using the 'system' Perl, and here is one solution. That is my opinion and a word of caution though, nothing wrong with Bio::DB::Sam. This is really what you should be using because the version of SAMtools mentioned above is really old and not being developed.

#SAMTOOLS MACOS HOMEBREW CODE#

I don't know what you are trying to do but I will mention that the fine folks over at EBI have developed bindings to htslib called Bio::DB::HTS based on Lincoln Stein's XS code in the Bio::DB::Sam module. That should get you a working Bio::DB::Sam. It is required on Linux, and since the module uses so much memory you will likely only be using this on a Linux machine. Note, the extra CFLAGS argument may not be needed on your Mac, so try without it first. The last command will allow you to install the Perl module without looking for the PATH to samtools and being prompted for it. I previously provided a solution to do this and I'll show a better way here (just use a package manager for the Perl module). This is an important point because you may run into issues using SAM/BAM files generated with samtools or other aligners because most tools use htslib these days.įor building the module, you are on the right track with the version you are using but it is difficult to build if you do not know the correct flags. The module Bio::DB::Sam provides bindings to an older version of samtools that did not rely htslib.

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#SAMTOOLS MACOS HOMEBREW HOW TO#

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#SAMTOOLS MACOS HOMEBREW MANUAL#

Or perhaps samtools is dependent on a static zlib library, in which case the manual build steps above should get you the static library. So if you're missing the library and header files, that might suggest some other issue with your computer. I'd think a normal OS X installation should have these zlib components available, however - at least the dylib. If you don't have these files, then you might manually install zlib components to /usr: $ cd /tmp You might check that you have libz.a or libz.dylib in /usr/lib and the associated header file zlib.h in /usr/include, where the samtools build tools can find them. Building them requires zlib development files to be installed on the build machine you may need to ensure a package such as zlib1g-dev (on Debian or Ubuntu Linux) or zlib-devel (on RPM/yum-based distributions) is installed. Samtools and HTSlib depend on the zlib library. The gzgetc() function is part of zlib, which is a dependency of samtools.

Samtools macos homebrew