Samtools installation on Mac OS X problems

Question

[Matt]

I am trying to install samtools-1.4.1 from http://www.htslib.org/download/ on Mac OS X El Capitan 10.11.6.

I can run ./configure and make without any errors, but make install results in the following error:

mkdir -p -m 755 /usr/local/bin /usr/local/bin /usr/local/share/man/man1
install: /usr/local/bin/samtools
No such file or directory
make: *** [install] Error 71

I ran sudo make install to get around this, and this proceeds without any error messages, but it results in the following programs in the bin folder:

ace2sam* maq2sam-long* plot-bamstats* seq_cache_populate.pl* zoom2sam.pl* blast2sam.pl* maq2sam-short* psl2sam.pl* soap2sam.pl* bowtie2sam.pl* md5fa* sam2vcf.pl* varfilter.py* export2sam.pl* md5sum-lite* samtools* wgsim* interpolate_sam.pl* novo2sam.pl* samtools.pl* wgsim_eval.pl*

To me this seems to be an incomplete list of programs, for example, faidx is missing.

Can anybody help on this?

Answer 1

[GenoMax]

faidx is an option for the samtools program. If you run ./samtools (from the directory above) on its own, you should get all possible program options.

Answer 2

[James Bonfield]

The previous answer is indeed most likely the main answer to your question, but regarding other issues you can use "make install prefix=/some/dir" to install in places other than /usr/local (or better yet, ./configure --prefix=/some/dir).

Also if using the joint samtools+htslib tarball you may find things like bgzip are missing. If you use those tools, run "make install-htslib" too as these aren't installed by default from the joint tarball.