The build finally worked on the downloaded source when adding to the
./configure command as proposed bu Rob and making use of the macport additional
libraries (likely from XZ).
I could build and install htslib, samtools , and bcftools v1.6 and have now
running samtools, bcftools and htsfile executables in my bin folder (and more
;-))
> ./configure CPPFLAGS='-I /opt/local/include’
Thanks to all for your help.
Stephane
<http://www.nucleomics.be/> Stephane Plaisance, Ph.D
Address: Herestraat 49, O&N4, Post Box 816, Room nr. 404-24 / 08.428, 3000
Leuven - Belgium
Tel: +32 (0)16 37 31 26
Lync: +32 (0)16 32 00 60
Fax: +32 (0)16 37 31 29
Web: www.nucleomics.be <http://www.nucleomics.be/>
> On 21 Nov 2017, at 13:03, samtools-help-requ...@lists.sourceforge.net wrote:
>
> Send Samtools-help mailing list submissions to
> samtools-help@lists.sourceforge.net
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://lists.sourceforge.net/lists/listinfo/samtools-help
> or, via email, send a message with subject or body 'help' to
> samtools-help-requ...@lists.sourceforge.net
>
> You can reach the person managing the list at
> samtools-help-ow...@lists.sourceforge.net
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Samtools-help digest..."
>
>
> Today's Topics:
>
> 1. Re: Issue Building htslib and samtools 1.6 on HighSierra OSX
> 10.13.1 (John Marshall)
> 2. Re: Issue Building htslib and samtools 1.6 on HighSierra OSX
> 10.13.1 (Robert Davies)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 20 Nov 2017 17:08:24 +0000
> From: John Marshall <john.w.marsh...@glasgow.ac.uk>
> To: VIB | Stephane Plaisance <stephane.plaisa...@vib.be>
> Cc: "samtools-help@lists.sourceforge.net"
> <samtools-help@lists.sourceforge.net>
> Subject: Re: [Samtools-help] Issue Building htslib and samtools 1.6 on
> HighSierra OSX 10.13.1
> Message-ID: <c7433d8c-9685-4986-81a0-059e1df06...@glasgow.ac.uk>
> Content-Type: text/plain; charset="us-ascii"
>
> On 17 Nov 2017, at 15:00, VIB | Stephane Plaisance
> <stephane.plaisa...@vib.be<mailto:stephane.plaisa...@vib.be>> wrote:
> I did install before but after upgrading to high Sierra I am lacking some dev
> dependencies (Xcode is installed)
> I tried installing xz using macport and got the error below (there is no port
> with -dev)
> [...]
> checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
> checking for lzma.h... no
> checking for lzma_easy_buffer_encode in -llzma... yes
>
> As the second "yes" here indicates, macOS does in fact natively include a
> liblzma shared library and in principle you should be able to use it without
> needing to install another XZ via Brew or MacPorts. However it does not
> provide the header files needed to compile code (like HTSlib) that uses the
> XZ functions. You might like to try applying this pull request:
>
> https://github.com/samtools/htslib/pull/628
>
> which adds the bare minimum to HTSlib to enable building against macOS's
> native liblzma.
>
> John
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 2
> Date: Mon, 20 Nov 2017 17:20:35 +0000 (GMT)
> From: Robert Davies <r...@sanger.ac.uk>
> To: VIB | Stephane Plaisance <stephane.plaisa...@vib.be>
> Cc: samtools-help@lists.sourceforge.net
> Subject: Re: [Samtools-help] Issue Building htslib and samtools 1.6 on
> HighSierra OSX 10.13.1
> Message-ID:
> <alpine.deb.2.10.1711201717540.3...@deskpro109045.internal.sanger.ac.uk>
>
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>
> On Fri, 17 Nov 2017, VIB | Stephane Plaisance wrote:
>
>> Thanks Robert for the rapid feedback, I tried but it die not fix it.
>> I seem to have an issue with gcc
>
> Ah, sorry. My instructions were wrong. It should have been:
>
> ./configure CPPFLAGS='-I /opt/local/include'
>
>
> This is what happens when you can't type it in first to check that it
> works...
>
>
> Rob Davies r...@sanger.ac.uk
> The Sanger Institute http://www.sanger.ac.uk/
> Hinxton, Cambs., Tel. +44 (1223) 834244
> CB10 1SA, U.K. Fax. +44 (1223) 494919
>
>
> --
> 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.
>
>
>
> ------------------------------
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> Samtools-help mailing list
> Samtools-help@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/samtools-help
>
>
> ------------------------------
>
> End of Samtools-help Digest, Vol 106, Issue 7
> *********************************************
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Samtools-help mailing list
Samtools-help@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/samtools-help
