[Bug 208943] biology/bowtie2: upgrade to 2.2.8

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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=208943

--- Comment #1 from Jason Bacon <bacon4000 at gmail.com> ---

Hi Joe,

Is there a specific feature or bug fix in 2.2.8 that you need?

There are several pipelines that depend on bowtie2, and they can be very
sensitive to changes in dependencies.  We'll need to test bowtie 2.2.8 with
trinity and tophat for starters before committing the upgrade.

In the future it might be better to add things like this as a -devel in my wip
collection before doing a PR:

https://github.com/outpaddling/freebsd-ports-wip

This will make testing changes quick and easy.

I can give you commit access if you're interested in adding to the collection. 
Otherwise, I'll add a bowtie2-devel myself using your patches and run the
trinity and tophat tests when I get a chance.

Regards,

   JB

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