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

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

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

[Message part 1 (text/plain, inline)]

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 #8 received at 47821 <at> debbugs.gnu.org (full text, mbox):

From: Efraim Flashner <efraim <at> flashner.co.il>
To: Roel Janssen <roel <at> gnu.org>
Cc: 47821 <at> debbugs.gnu.org
Subject: Re: [bug#47821] [PATCH] Update htslib, bcftools, samtools, bedtools
Date: Tue, 27 Apr 2021 10:32:13 +0300

[Message part 1 (text/plain, inline)]

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.

-- 
Efraim Flashner   <efraim <at> flashner.co.il>   אפרים פלשנר
GPG key = A28B F40C 3E55 1372 662D  14F7 41AA E7DC CA3D 8351
Confidentiality cannot be guaranteed on emails sent or received unencrypted

[signature.asc (application/pgp-signature, inline)]

Message #11 received at 47821 <at> debbugs.gnu.org (full text, mbox):

From: Roel Janssen <roel <at> gnu.org>
To: Efraim Flashner <efraim <at> flashner.co.il>
Cc: 47821 <at> debbugs.gnu.org
Subject: Re: [bug#47821] [PATCH] Update htslib, bcftools, samtools, bedtools
Date: Wed, 28 Apr 2021 16:05:09 +0200

[Message part 1 (text/plain, inline)]

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 (text/x-patch, attachment)]

Message #14 received at 47821 <at> debbugs.gnu.org (full text, mbox):

From: Efraim Flashner <efraim <at> flashner.co.il>
To: Roel Janssen <roel <at> gnu.org>
Cc: 47821 <at> debbugs.gnu.org
Subject: Re: [bug#47821] [PATCH] Update htslib, bcftools, samtools, bedtools
Date: Thu, 29 Apr 2021 09:43:35 +0300

[Message part 1 (text/plain, inline)]

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.


-- 
Efraim Flashner   <efraim <at> flashner.co.il>   אפרים פלשנר
GPG key = A28B F40C 3E55 1372 662D  14F7 41AA E7DC CA3D 8351
Confidentiality cannot be guaranteed on emails sent or received unencrypted

[signature.asc (application/pgp-signature, inline)]

Message #19 received at 47821-done <at> debbugs.gnu.org (full text, mbox):

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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