[Samtools-help] Install problems

[Matt Evans]

Hello,

I am trying to install samtools on Mac OS X El Capitan 10.11.6.
Downloading samtools-1.4.1 from http://www.htslib.org/download/ <http://www.htslib.org/download/>, I run the following commands:

./configure --disable-lzma # I did this because I was getting an error without it, and the INSTALL guide recommended this.
make
make prefix=usr/local install

This runs fine without any error messages, but when I look at what’s sitting in the resulting bin folder, only a limited selection of tools are there (below), and trying to execute them results in a ‘command not found’ error message.

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

Could anybody help me with this?

Many thanks,
Matt