[Neurodebian-users] Developer files for Debian FSL

[Yaroslav Halchenko]

On Thu, 19 Jun 2014, Dillon Niederhut wrote:
>    Thanks for the comments! Sorry for not being more precise. I installed FSL
>    from the neurodebian repo, and all the normal stuff works fine. The good
>    folks at FMRIB have sent me some experimental analysis tools that require
>    setup and compiling. I could not get them to compile using the files and
>    instructions they sent. The readme essentially says to untar the folder
>    (which contains a makefile, dependencies, etc), run 
>    $ . setup.sh 
>    , then run 
>    $ make 
>    It seems that my installation is lacking "a compatible devel package",
>    which has the default make, config, and include files that the setup
>    scripts were expecting.
>    I've been told that I have two options:
>    1. Uninstall neurodebian FSL and try to build the source FSL myself

probably not even needed to uninstall neurodebian FSL since it is not in
the way unless you source /etc/fsl/fsl.sh.

>    2. Download the source version of FSL, then customize those config files
>    to match the neurodebian libraries and executables

I guess you could indeed

a. fakeroot debian/rules install # should build and install under debian/
b. and then build your custom tool using this freshly built fsl


>    My questions would more precisely have been stated as:
>    1. Does neurodebian already have the FSL devel package? If so, how can I
>    install it?

not that I am aware of, Michael would know better

>    2. If not, is there documentation on editing source FSL config files to
>    work with neurodebian?

all the patches are under debian/patches and all the 'build' steps are
within debian/rules -- but that one is quite "evolved" by now

>    I've attached the makefile, in case that will be of any help. 
>    Running:
>    $ sudo apt-get build-dep fsl
>    throws this dependency error:
>    <The following packages have unmet dependencies:
>     libgd2-noxpm-dev : Depends: libgd2-noxpm (= 2.0.36~rc1~dfsg-6ubuntu2) but
>    it is not going to be installed

what is output of 

apt-cache policy libgd2-noxpm-dev libgd2-noxpm


?

-- 
Yaroslav O. Halchenko, Ph.D.
http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org
Research Scientist,            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