From: John M. <jm...@sa...> - 2013-11-20 11:19:25
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On 19 Nov 2013, at 23:46, Robert Davies wrote: > 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 That is the current default place for it; probably the only thing you were missing, as Rob noted, is that currently you need the develop branch of htslib too. > 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've now made develop the default branch for htslib too, so you'll get the current code by default in future git clones. Apologies for the confusion. > 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. +1 At the moment, this is a work-in-progress and the build process is a bit rough. As we move closer to making a formal release, we're planning to add a configure script to make htslib-finding more flexible and less mysterious. The eventual release samtools and bcftools source tarballs will also contain their own copies of htslib (to be used optionally; if you already have htslib installed you'll probably prefer to use that), so will be as easy to build as previous stable releases. John -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. |