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

[Roel Janssen]

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?

Kind regards,
Roel Janssen

0005-gnu-Update-python-pybedtools-to-0.8.2.patch
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