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?