Re: linuxbrew with homebrew/science - works!
Hello and apologies for the delay
[adding Tim to Cc since he was addressed in Steffen's last message]
على الأحد 31 تـمـوز 2016 15:07، كتب Steffen Möller:
>
>
> On 30/07/16 10:15, Afif Elghraoui wrote:
>> Hi, all,
>>
>> على الخميس 28 تـمـوز 2016 03:54، كتب Sascha Steinbiss:
>>>> I do not know what this means for Debian Med. It is a competition. And,
>>>>> with some early brain wash from the homebrew on the Mac I am now using
>>>>> on my desk, it also feels natural.
>> I personally would prefer a way to adapt our Debian packages for this
>> purpose. Surely, some of the effort for the packaging is duplicated
>> between us, the linuxbrew, and the conda people (not to mention just
>> other Linux distributions in general). If we can make Debian packages
>> installable without root permissions into user-specified directories,
>> our packages will have much more utility both in Debian and in other
>> operating systems.
> I basically see two possible forms of a transition:
> A) dotdeb2bottle - so we would have some generic formula that takes a
> .deb, unpacks it in #{prefix} and hopes that the symlinks just work
> or does some post-processing.
> @Tim, are you listening? The _old_ pre-2010 Bio-Linux way was to
> basically create its debs by taking a Brew-like bottle and wrap it up
> as a .deb. So, a formula doing it all backwards should be fine.
I don't think Tim follows the list, but is Cc'd here now.
> B) debian2formula - This is a bit more tricky. We have the download URL,
> preferably via watch, the one-lined description, the doi, the
> bioinformatics
> tag, the install instructions, the dependencies ... maybe we have a bit
> too many binary and arch-indep packages ... but one could for
> quite some
> packages find rewrites, I presume.
>
> What if we just changed debhelper install to the Formula's #{prefix}
> instead of debian/<packagename>?
>>
I like your suggestion A best. I think extracting the package contents
to the installation location would be better than building the package
directly into it.
>>>
>>> Something I personally find interesting about Homebrew-science (but
>>> others here may disagree) is that they apparently have a more relaxed
>>> way of embracing upstream's way of distribution and building, which
>>> seems to accelerate turnover time for packaging a lot. For example,
>>> there is no requirement to build in a non-networked environment using
>>> already packaged dependencies only. While I am aware of the security and
>>> long-term maintainability considerations, this is difficult to beat for
>>> the pure purpose of distribution and easy installability, and indeed I
>>> have often seen their list of recipes contain new tools much earlier
>>> than Debian.
>> Indeed. One of my strongest motivations for being involved in Debian is
>> the integration that we do. While we can't have official packages that
>> follow such relaxed requirements, we might keep up in this regard with
>> some unofficial ([semi-]auto-generated? [1]) packages, but I think our
>> main problem is lack of support for unprivileged installation.
> I am with you, here. Avoiding redundant libraries is a major contributor
> to bring in scientific progress early. One is tempted to I think that as
> soon as developers recognize that with homebrew everyone can (even
> OS-independently) get the library installed, the motivation to redistribute
> external sources will weaken. But IMO the problem is less a matter of
> commodity
> than with a distrust in stable APIs.
>
That sounds about right, but I'm not sure what to say to that.
Thanks and regards
Afif
--
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name
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