On Tue, Apr 29, 2014 at 2:59 PM, Dave Bouvier <dave@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_dependen... Regards, Peter