bug#47821: [PATCH] Update htslib, bcftools, samtools, bedtools

[Roel Janssen]

On 4/29/21 8:43 AM, Efraim Flashner wrote:
> On Wed, Apr 28, 2021 at 04:05:09PM +0200, Roel Janssen wrote:
> > On Tue, 2021-04-27 at 10:32 +0300, Efraim Flashner wrote:
> > > On Fri, Apr 16, 2021 at 11:55:39AM +0200, Roel Janssen wrote:
> > > > Hi Guix,
> > > >
> > > > The following patches update htslib, bcftools, samtools, and
> > > > bedtools.
> > > > I've succesfully built bedtools with the latest samtools instead of
> > > > the
> > > > 1.9 version.
> > > These look good and are ready for merging. Can you take a look at
> > > python-pybedtools? There's a new version out which I hope builds with
> > > the newer version of bedtools.
> > >
> > > Thanks.
> > I looked at python-pybedtools and came up with the following patch.
> > The test phase is still not entirely happy because it ends with:
> >
> > ---
> > ================ 497 passed, 3 xfailed, 426 warnings in 25.49s
> > =================
> > Error in atexit._run_exitfuncs:
> > Traceback (most recent call last):
> >    File "/gnu/store/rz42ba0my9vrgbkjpkzr2drmnjk5ah50-python-
> > 3.8.2/lib/python3.8/shutil.py", line 704, in rmtree
> >      orig_st = os.lstat(path)
> > ---
> >
> > I attached the patch that I have that at least builds the newer version
> > of python-pybedtools.  I don't know how to further test it.
> >
> > Can I in the meantime already push the patches for updating htslib,
> > bcftools, samtools and bedtools?
> Yeah, those patches LGTM.
Thanks. I pushed these.

For python-pybedtools, I think a little bit more testing is required.  I 
can take a look at it in the second week of May, so hopefully someone 
beats me to it. :)

Kind regards,
Roel Janssen