From: Roel Janssen <roel@gnu.org>
To: zimoun <zimon.toutoune@gmail.com>, 44613@debbugs.gnu.org
Subject: [bug#44613] [PATCH] Fix build for bedtools
Date: Fri, 13 Nov 2020 13:55:29 +0100 [thread overview]
Message-ID: <695715d9f08a7ec06b6dfe8bcf71173829a0d029.camel@gnu.org> (raw)
In-Reply-To: <86v9e9e8gz.fsf@gmail.com>
Hi Simon,
On Fri, 2020-11-13 at 13:39 +0100, zimoun wrote:
> Hi Roel,
>
> On Fri, 13 Nov 2020 at 12:01, Roel Janssen <roel@gnu.org> wrote:
>
> > With the following patches, I'd like to add samtools-1.9, htslib-
> > 1.9
> > (samtools depends on that) to fix this problem with bedtools.
>
> Recently, investigating why the substitute of ’python-pysam’ was not
> available, I decided then to give a try at fixing the TODO:
>
> --8<---------------cut here---------------start------------->8---
> (snippet '(begin
> ;; Drop bundled htslib. TODO: Also remove
> samtools
> ;; and bcftools.
> (delete-file-recursively "htslib")
> #t))))
> --8<---------------cut here---------------end--------------->8---
>
> And the bundled version is 1.9 (if I remember correctly), therefore
> because of:
>
> --8<---------------cut here---------------start------------->8---
> (native-inputs
> `(("python-cython" ,python-cython)
> ;; Dependencies below are are for tests only.
> ("samtools" ,samtools)
> ("bcftools" ,bcftools)
> ("python-nose" ,python-nose)))
> --8<---------------cut here---------------end--------------->8---
>
> some tests are unhappy.
>
> That’s said, these additions seem fine with me. :-)
>
I also tried removing the bundled htslib for bedtools, but didn't go
this route for two reasons:
- The bundled htslib for bedtools seems "slightly modified" (I didn't
investigate further)
- Replacing the references to libhts.a with $(pkg-config htslib --
cflags --libs) produced various linker errors. So I stopped right
there.
I'm sure more tools will likely have failed because of the htslib
upgrade (sorry about this!), so having htslib-1.9 around for some time
may be a good fallback for now.
Just to double-check: Is it OK to push the proposed patches?
Kind regards,
Roel Janssen
next prev parent reply other threads:[~2020-11-13 12:56 UTC|newest]
Thread overview: 7+ messages / expand[flat|nested] mbox.gz Atom feed top
2020-11-13 11:01 [bug#44613] [PATCH] Fix build for bedtools Roel Janssen
2020-11-13 12:39 ` zimoun
2020-11-13 12:55 ` Roel Janssen [this message]
2020-11-13 13:34 ` zimoun
2020-11-13 14:00 ` bug#44613: " Roel Janssen
2020-11-13 15:08 ` [bug#44613] " Marius Bakke
2020-11-13 15:51 ` [bug#44613] what “guix build -S” should return? zimoun
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