Three new Bioinformatics packages, just version bumps

I just used the existing 1.4.10 goolf toolchain that was already used for previous versions and bumped to the newest version that compiled cleanly.

I plan to work on migrating these to a newer gcc based toolchain.

Not sure if the commits should be cleaner.
Actually, please don't upgrade that one ;-)

Whomever things that Boost/M.N+1 is compatible with Boost/M.N, raise your
hands, I need to see you!
:-P

About Author: I recommend to add your name in there (or replace the
others); so people know who to ask if they want clarifications for how that
easyconfig is expected behave on their sites.
(that communication is an advantage for both sides)

fyi.
`biodeps` has confined versions of dependencies, intentionally, so that
bioinformaticians can easily
mix-n-match modules for building more complex pipelines (other scientists
rarely ever have this need).
Most bioinfo packages (used to) be compatible with the biodeps definitions.

So far, the most popular toolchains for bioinformatics have proved to be
`goolf/1.4.10` & `ictce/5.3.0`;
however, at some point they will also have to be advanced forward (in both
major and minor),
in order to take advantage of more modern compilers' features (gnu &
intel). Ditto for biodeps.

btw. you may wish to try `eb HPCBIOS_Bioinfo*eb --try-toolchain=X,Y -r` to
build a bunch of bioinformatics packages against a given toolchain;
confining a biodeps set is a prereq for that, too.



On Sat, Nov 8, 2014 at 6:47 PM, Robert Schmidt <notifications@github.com>
wrote:

> In easybuild/easyconfigs/t/TopHat/TopHat-2.0.12-goolf-1.4.10.eb:
>
> > +##
> > +
> > +name = 'TopHat'
> > +version = '2.0.12'
> > +
> > +homepage = 'http://ccb.jhu.edu/software/tophat/'
> > +description = """TopHat is a fast splice junction mapper for RNA-Seq reads."""
> > +
> > +toolchain = {'name': 'goolf', 'version': '1.4.10'}
> > +toolchainopts = {'optarch': True, 'pic': True}
> > +
> > +sources = [SOURCELOWER_TAR_GZ]
> > +source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/']
> > +
> > +dependencies = [
> > +    ('Boost', '1.51.0', '-Python-2.7.3'),
>
> There doesn't seem to be a boost version 1.55 built in the same way. I'll
> definitely do that though in the next iteration.
>
> The idea was just to pull it forward versions as simply as possible so I
> would have a baseline. I'm also wondering if I should clarify the Author:
> heading.
>
> I'll reach out to the list and/or IRC to get some advice on which goolf
> version is preferred. A lot of stuff is being build ictce, but our main
> node is AMD so I would rather avoid that without some more testing.
>
> —
> Reply to this email directly or view it on GitHub
> <https://github.com/hpcugent/easybuild-easyconfigs/pull/1186/files#r20053008>
> .
>



-- 


echo "sysadmin know better bash than english"|sed s/min/mins/ \
  | sed 's/better bash/bash better/' # signal detected in a CERN forum