Re: Bowtie upgrade to version 1.3
Hi Jun,
On Tue, Sep 15, 2020 at 02:00:09PM +0200, Jun Aruga wrote:
> > It seems the Python3 patch was applied, some others as well and there
> > seems also be a relevant change for our patches since SeqAn seems not to
> > be used any more. So I removed or deactivated all patches with some
> > connection to SeqAn.
>
> Hi Andreas, thanks for working on it.
:-)
> Yes. SeqAn dependency was removed on bowtie 1.3.0, as I adjusted it
> with the upstream.
> I remember the bowtie deb package has a patch to build with the SeqAn in Debian.
> So, I believe this change makes the packaging easier.
Sure, we get rid of some patches which is always nice. I could have
saved some time if I would have known in advance and would not have went
through all the patches step by step - but anyway, its easier now.
> > I was wondering about those /usr/bin/bowtie*-debug binaries. Do we
> > *really* need these? Some of them (namely bowtie-inspect-*-debug
> > seem to be perfectly identical to their non-debug counterparts). IMHO
> > we are bloating user machines with some data load that is not used
> > (and also not installed by the default bowtie installation procedure -
> > I had to add these explicitly after noticing the diff in the debdiff).
>
> In my understanding, the `*-debug` binaries are used inside the bowtie
> binary when it is called as `bowtie --debug`.
> (bowtie2 is the same as well).
>
> > IMHO the bowtie-dbgsym package is providing the functionality of those
> > additional executables and I think these extra binaries should not be
> > shipped inside the bowtie package.
>
> I agree on your idea to include the -debug binaries in a bowtie-foo
> sub package, not in the bowtie main package.
Ok, so needed, but not in most cases. The problem is that I'm currently
scared about rejections in new queue - so for the moment I will not
change the package structure for this very reason.
Thanks a lot for your comments
Andreas.
--
http://fam-tille.de
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