Re: [Samtools-devel] Compiling from Github develop branch

[Robert D. <rmd...@sa...>]

On Tue, 19 Nov 2013, Peter Chines wrote:

> Hello, can someone briefly describe how git working directories should
> be arranged and any other configuration necessary in order to
> successfully build samtools from the Github develop branch?
>
> I have tried cloning the htslib repo into the same parent directory as
> samtools, and even made an htslib symlink within the samtools directory
> to try to get the header files where they seem to be desired.

You should be able to do it like this:

git clone -b develop https://github.com/samtools/htslib.git htslib
git clone -b develop https://github.com/samtools/samtools.git samtools
cd samtools
make

(The makefile in samtools includes a rule to build htslib as well.)

It's important to make sure you have the 'develop' branch of both 
check-outs.  By default you get 'master' for htslib, which can lead to 
some confusion if you don't realise that has happened.

> I know that someone out there must be building from this branch, and
> would appreciate any hints on how this should be done.  In return, I
> would be happy to add the answer to the FAQ page of the wiki.

It would be worth pointing out that develop is a work-in-progress, so not 
the a good choice for end-users after a stable version.  The stable 
versions are, as I understand it, still being released as tarballs on 
sourceforge.

Rob Davies              rm...@sa...
The Sanger Institute    http://www.sanger.ac.uk/
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