From: Roel Janssen <roel@gnu.org>
To: Efraim Flashner <efraim@flashner.co.il>
Cc: 47821-done@debbugs.gnu.org
Subject: bug#47821: [PATCH] Update htslib, bcftools, samtools, bedtools
Date: Thu, 29 Apr 2021 12:21:37 +0200 [thread overview]
Message-ID: <42f9d1f0-88d6-beb7-81c1-ef1b0e501ff2@gnu.org> (raw)
In-Reply-To: <YIpVlwfoX5gK7Uez@3900XT>
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
prev parent reply other threads:[~2021-04-29 10:22 UTC|newest]
Thread overview: 5+ messages / expand[flat|nested] mbox.gz Atom feed top
2021-04-16 9:55 [bug#47821] [PATCH] Update htslib, bcftools, samtools, bedtools Roel Janssen
2021-04-27 7:32 ` Efraim Flashner
2021-04-28 14:05 ` Roel Janssen
2021-04-29 6:43 ` Efraim Flashner
2021-04-29 10:21 ` Roel Janssen [this message]
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