On Tue, Apr 29, 2014 at 2:59 PM, Dave Bouvier <d...@bx.psu.edu> wrote:
> Peter,
>
> Based on the latest test run, and my own investigations, it would appear
> that the samtools compilation process is looking in the wrong include path
> for ncurses/ncurses_dll.h. My recommendation would be to replace the
> following:
>
> -I$NCURSES_INCLUDE_PATH/ncurses/
>
> with
>
> -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH
>
> in the shell_command for package_samtools_0_1_19's tool_dependencies.xml
> that starts with: sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|
>
>   --Dave B.

Thanks Dave,

That sounds like it would be more robust to subtle server changes.

I see Bjoern has been working on this today with a slightly different
change - I'll leave this in his capable hands:

https://github.com/bgruening/galaxytools/commits/master/orphan_tool_dependencies/package_samtools_0_1_19/tool_dependencies.xml

Regards,

Peter
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