Question: Samtools installation on Mac OS X problems
gravatar for Matt
12 months ago by
Queen's University Belfast
Matt10 wrote:

I am trying to install samtools-1.4.1 from 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**** maq2sam-short**** md5fa**** md5sum-lite* samtools* wgsim*****

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

Can anybody help on this?

samtools mac software error • 1.9k views
ADD COMMENTlink modified 11 months ago by James Bonfield120 • written 12 months ago by Matt10
gravatar for genomax
12 months ago by
United States
genomax49k wrote:

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.

ADD COMMENTlink modified 12 months ago • written 12 months ago by genomax49k
gravatar for James Bonfield
11 months ago by
James Bonfield120 wrote:

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.

ADD COMMENTlink written 11 months ago by James Bonfield120
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