Bug#925499: bowtie2 arm64 (aarch64) package

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Bug#925499: bowtie2 arm64 (aarch64) package

Jun Aruga
Source: bowtie2
Severity: wishlist

Dear bowtie2 maintainer,

As the latest version bowtie2 2.3.5 started to support arm64 (aarch64) as a
experiment.
Is it possible for you to prepare bowtie2 arm64 (aarch64) deb pacakge?

Here is my contribution to support it on the bowtie2 upstream project.
https://github.com/BenLangmead/bowtie2/pull/216
You can refer how to build it by seeing Makefile.

We need a patch to the source code.
See 4 sed commands in the bottom part of Dockerfile-aarch64.

Thank you.





-- System Information:
Debian Release: 9.8
  APT prefers stable-updates
  APT policy: (500, 'stable-updates'), (500, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 4.9.0-8-amd64 (SMP w/1 CPU core)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

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Bug#925499: bowtie2 arm64 (aarch64) package

Michael Crusoe
Hello Jun,
 
Thank you for your report and for your work to improve the architecture support on several projects!

I think this is a good idea for after the "buster" release. Could you prepare a pull request at https://salsa.debian.org/med-team/bowtie2 and we can merge it then?

Alternatively we could do a build in the experimental suite, and then you could test building all the packages that have a build-time or run-time dependency on bowtie2 under aarch64. I have a feeling that we may need to adjust some (many?) other packages which is why I advocate for this to wait for the next release cycle. If it goes well, then we could backport the adjustments (or propose for the "buster.1" point release).

$ apt-cache rdepends bowtie2
bowtie2
Reverse Depends:
  ariba
  unicycler
  trinityrnaseq
 |tophat
  srst2
  rsem
  python-pbalign
  pbalign
  paleomix
  metaphlan2-data
  metaphlan2
  giira
  gasic

Cheers,

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Bug#925499: [Debian-med-packaging] Bug#925499: bowtie2 arm64 (aarch64) package

Alex Mestiashvili-4
Hi All,

as far as I see, we need to get SIMDe into Debian before we can build
bowtie2 for ARM64.
See:
https://github.com/BenLangmead/bowtie2/commit/4213c394cb21311e01c4a8e8778e27980c38d0be

Best,
Alex

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Bug#925499: [Debian-med-packaging] Bug#925499: bowtie2 arm64 (aarch64) package

Jun Aruga
Hi Michael and Alex

I am happy to contribute to the Debian med team community.
However I am new in Debian community. I need a time to learn how to
package a deb package.
I am sorry I have to say that I am busy now and I have no capacity to do it.

The steps to a patch could be like this.

1. Update bowtie2 to the latest version 2.3.5.
2. Packaging simde.
3. Patch to run bowtie2 on arm64 (aarch64).

Jun

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Bug#925499: Bug#925499: bowtie2 arm64 (aarch64) package

Andreas Tille-6
Hi Jun,

On Fri, Mar 29, 2019 at 08:35:34PM +0100, Jun Aruga wrote:
> I am happy to contribute to the Debian med team community.

:-)

> However I am new in Debian community. I need a time to learn how to
> package a deb package.

We have a mentoring program in the Debian Med team to teach packaging:

    https://wiki.debian.org/DebianMed/MoM

> I am sorry I have to say that I am busy now and I have no capacity to do it.
>
> The steps to a patch could be like this.
>
> 1. Update bowtie2 to the latest version 2.3.5.
> 2. Packaging simde.

If you want to try packaging

   https://github.com/nemequ/simde.git

in a MoM project feel free to let me know.  It seems you are qualified
in terms of beeing easily able to test it with bowtie2 on arm64
hardware.

I'd happily support your attempt to learn packaging in MoM project

     Andreas.


--
http://fam-tille.de

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Bug#925499: Bug#925499: bowtie2 arm64 (aarch64) package

Jun Aruga
Hi Andreas,

Sorry for the late response.
Thanks for showing the mentoring program. I will look at the MoM.

> If you want to try packaging
>
>    https://github.com/nemequ/simde.git
>
> in a MoM project feel free to let me know.  It seems you are qualified
> in terms of beeing easily able to test it with bowtie2 on arm64
> hardware.

Andreas, I want to try the packaging of simde and bowtie2 to support Arm64.

At this moment, I just have the virtual arm64 environment. But near
future I am going to have a native arm64 server.
I also have some ways to test on arm64.

There is Works on Arm service that is to provide "free" aarch64 server
for mainly open source project.
I might recommend you to apply below server as DebianMed team, though
I do not know if we can use Debian on the server.
I think DebianMed team is qualified for that.

Works on Arm
https://www.worksonarm.com/cluster/

By the way, for the steps to support bowtie2 arm64.

> 3. Patch to run bowtie2 on arm64 (aarch64).

Yesterday, my pull-request to run bowtie2 on arm64 without a patch was merged.
It will be included in the coming next version of bowtie2. Yes! :)
https://github.com/BenLangmead/bowtie2/commit/c6a6648fcd05bff0e5ca64a305bb1c488beacbcf

So, now only below 2 steps.

* Packaging simde.
* Update bowtie2 to the latest version 2.3.5.

Jun

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Bug#925499: bowtie2 arm64 (aarch64) package

Andreas Tille-5
Hi Jun,

On Tue, Apr 16, 2019 at 09:17:59AM +0200, Jun Aruga wrote:
> Thanks for showing the mentoring program. I will look at the MoM.

:-)
 
> > If you want to try packaging
> >
> >    https://github.com/nemequ/simde.git
> >
> > in a MoM project feel free to let me know.  It seems you are qualified
> > in terms of beeing easily able to test it with bowtie2 on arm64
> > hardware.
>
> Andreas, I want to try the packaging of simde and bowtie2 to support Arm64.

Good!

> At this moment, I just have the virtual arm64 environment. But near
> future I am going to have a native arm64 server.
> I also have some ways to test on arm64.
>
> There is Works on Arm service that is to provide "free" aarch64 server
> for mainly open source project.
> I might recommend you to apply below server as DebianMed team, though
> I do not know if we can use Debian on the server.
> I think DebianMed team is qualified for that.

It might be interesting for the members of the team to have easy
access to some arm64 server.  (CCing Debian Med mailing list for
this information.)

> Works on Arm
> https://www.worksonarm.com/cluster/
>
> By the way, for the steps to support bowtie2 arm64.
>
> > 3. Patch to run bowtie2 on arm64 (aarch64).
>
> Yesterday, my pull-request to run bowtie2 on arm64 without a patch was merged.
> It will be included in the coming next version of bowtie2. Yes! :)
> https://github.com/BenLangmead/bowtie2/commit/c6a6648fcd05bff0e5ca64a305bb1c488beacbcf
>
> So, now only below 2 steps.
>
> * Packaging simde.
> * Update bowtie2 to the latest version 2.3.5.

The latter step is usually pure routine.

Kind regards

      Andreas.

--
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