GNU bug report logs - #47821
[PATCH] Update htslib, bcftools, samtools, bedtools

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Roel Janssen <roel <at> gnu.org>
Cc: tracker <at> debbugs.gnu.org
Subject: bug#47821: closed ([PATCH] Update htslib, bcftools, samtools,
 bedtools)
Date: Thu, 29 Apr 2021 10:22:02 +0000

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Your message dated Thu, 29 Apr 2021 12:21:37 +0200
with message-id <42f9d1f0-88d6-beb7-81c1-ef1b0e501ff2 <at> gnu.org>
and subject line Re: [bug#47821] [PATCH] Update htslib, bcftools, samtools, bedtools
has caused the debbugs.gnu.org bug report #47821,
regarding [PATCH] Update htslib, bcftools, samtools, bedtools
to be marked as done.

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From: Roel Janssen <roel <at> gnu.org>
To: guix-patches <at> gnu.org
Subject: [PATCH] Update htslib, bcftools, samtools, bedtools
Date: Fri, 16 Apr 2021 11:55:39 +0200

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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.

Kind regards,
Roel Janssen

[0004-gnu-Update-bedtools-to-2.30.0.patch (text/x-patch, attachment)]

[0003-gnu-Update-samtools-to-1.12.patch (text/x-patch, attachment)]

[0002-gnu-Update-bcftools-to-1.12.patch (text/x-patch, attachment)]

[0001-gnu-htslib-Update-to-1.12.patch (text/x-patch, attachment)]

[Message part 8 (message/rfc822, inline)]

From: Roel Janssen <roel <at> gnu.org>
To: Efraim Flashner <efraim <at> flashner.co.il>
Cc: 47821-done <at> debbugs.gnu.org
Subject: Re: [bug#47821] [PATCH] Update htslib, bcftools, samtools, bedtools
Date: Thu, 29 Apr 2021 12:21:37 +0200

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

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