Sadly, <action type="shell_command">./configure --disable-gui --prefix=$INSTALL_DIR</action> yeilds install error: /bin/sh: ./configure: No such file or directory But file must be there since previous git step is carried out ok: ... ############################################# git reset --hard 1819482db93bf0025c2588b5264cc0ec8c61029c STDOUT HEAD is now at 1819482 Added gitignore ############################################# git reset --hard 1819482db93bf0025c2588b5264cc0ec8c61029c STDERR ############################################# ./configure --disable-gui --prefix=/usr/local/galaxy/shared/tool_dependency/ffp-phylogeny/0.3.19_1819482db93bf0025c2588b5264cc0ec8c61029c/ddooley/ffp_phylogeny/4e213eee0fef STDOUT ############################################# ./configure --disable-gui --prefix=/usr/local/galaxy/shared/tool_dependency/ffp-phylogeny/0.3.19_1819482db93bf0025c2588b5264cc0ec8c61029c/ddooley/ffp_phylogeny/4e213eee0fef STDERR /bin/sh: ./configure: No such file or directory ############################################# argh! d. ________________________________________ From: Aaron Petkau [aaron.petkau@gmail.com] Sent: Friday, August 01, 2014 11:47 AM To: Dooley, Damion Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Toolshed tool_dependency.xml git archive configure issue Hey Damion, You should be able to do ./configure --disable-gui ... to get it to work (that is, make sure the full path to the configure command is given). At least I think that's probably what's going on. Aaron