Re: [AMOS-help] AMOS compilation hard-code paths + ignore DELTAFILTER and SHOWCOORDS

[Martin M. <mmo...@fo...>]

Hi Joel,
  thanks for sharing this information. While I am not an AMOS developer let me mention
these two patches Gentoo Linux uses and which might be of interest to you:
  http://sources.gentoo.org/cgi-bin/viewvc.cgi/gentoo-x86/sci-biology/amos/files/

Regards,
Martin

Joel Fillon, Mr wrote:
> Hi AMOS developers,
> 
> I don't know if AMOS is still maintained but I'm trying to compile it (version 3.1.0) and I have 2 problems:
> 
> 1. AMOS hard-codes dependency paths for Perl, Python, MUMmer, UCSC tools.
> Since we use modules with possibly different dependencies versions,
> it would be nice to compile it with simple command names and let the user add the commands in the $PATH as he wants.
> 
> 2. As a workaround, I compile it as:
> 
>   ./configure \
>     PERL=`which perl` \
>     PYTHON=`which python` \
>     NUCMER=`which nucmer` \
>     DELTAFILTER=`which delta-filter` \
>     SHOWCOORDS=`which show-coords` \
>     BLAT=`which blat` \
>     --prefix=$INSTALL_DIR/$SOFTWARE_DIR \
>     --with-qmake-qt4=/usr/lib64/qt4/bin/qmake
>   make
>   make install
> 
> but DELTAFILTER and SHOWCOORDS seem to be ignored since they create a default invalid path.
> 
> Afterwards, I set the proper paths with:
> 
>   perl -pi -e s,"DELTAFILTER\s+=.*,DELTAFILTER=`which delta-filter`,g" bin/minimus2
>   perl -pi -e s,"SHOWCOORDS\s+=.*,SHOWCOORDS=`which show-coords`,g" bin/minimus2
> 
> Any ideas?
> 
> Thanks for your help,
> Joël