[Neurodebian-users] installing cmtk without sri24-atlas

[Yaroslav Halchenko]

Hi Gregory,

On Wed, 19 Feb 2014, Gregory Jefferis wrote:

> Recently we have been setting up continuous integration with travis for an R package
> 	https://travis-ci.org/jefferis/nat
> which depends on CMTK. We are installing cmtk from neurodebian:
> 	http://neuro.debian.net/pkgs/cmtk.html
> Thanks guys!

you are welcome!

> Unfortunately 90% of the build time is spent downloading 60Mb of sri24-atlas, which is irrelevant for our tests. It appears that cmtk depends on sri24-atlas but I don't see why it should (I would have thought sri24-atlas would be a suggested package).

ah -- nice!  I thought I never finished/released that package  but I
guess I meant only FSLview of it which I still only locally...

> Is there any reason for this dependency? 

some parts of cmtk make use of it AFAIK, so in general sri24
should accompany cmtk.  that is why it is in Recommends.

> Is there any way I can avoid installing the sri24-atlas? 

sudo apt-get install cmtk --no-install-recommends

;)


> Also while I am asking, is there a way to set a mirror preference order (the US mirrors are likely quite a bit faster than e.g. Munich which was chosen for the last build).

SURE -- just specify both mirrors in one file with first one being of
preference... at some point amazon provided us some credits for mirror in S3,
and I kept syncing it there from time to time, so eventually we should
formalize it and make available publicly - may be it would be the most
efficient for travis.

also for travis you can use 1 liner setup now

    - bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)

which should get preferred mirror (for now original us-nh, but later we might
switch at once to use amazon)

Now my quick question to you Gregory:

what system do you use for monitoring/filming your flies behavior (positions,
trajectories)? or you don't?

Some young fellas stopping at our booth at SfN  were interested if there are
reasonable and open systems for monitoring motion of e.g. toads, so I
wondered to ask since myself I have no experience in non-human fields.

Cheers!
-- 
Yaroslav O. Halchenko, Ph.D.
http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org
Senior Research Associate,     Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik