Hi All, I have a galaxy installation on an OSX system that has been running fine with our custom tools. However, now we want to start using for some simple BAC mapping. When I go to the main toolshed to install bwa, it lists the following dependencies. Repository *package_bwa_0_7_10_039ea20639* revision *5b9aca1e1c07* owned by *devteam*Repository *package_samtools_1_1* revision *43f2fbec5d52* owned by *iuc* However, when running through this process, it fails at the package_samtools_1_1 stage with an Error. Looking at the INSTALLATION.LOG i see the following. ############################################# sed -i 's/-lcurses/-lncurses/' Makefile STDOUT ############################################# ############################################# sed -i 's/-lcurses/-lncurses/' Makefile STDERR sed: 1: "Makefile": invalid command code M ############################################# However, looking at the tool_dependencies.xml for this particular package, I see the following. I've highlighted in yellow a key configuration. <?xml version="1.0"?> <tool_dependency> <package name="samtools" version="1.1"> <install version="1.0"> <actions_group> <actions architecture="x86_64" os="linux"> <action type="download_by_url"> http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-1.1-Li... </action> <action type="move_directory_files"> <source_directory>.</source_directory> <destination_directory>$INSTALL_DIR</destination_directory> </action> </actions> <actions> <package name="ncurses" version="5.9"> <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="zlib" version="1.2.8"> <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <action type="download_by_url"> http://downloads.sourceforge.net/project/samtools/samtools/1.1/samtools-1.1.... </action> <action type="set_environment_for_install"> <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" toolshed=" https://toolshed.g2.bx.psu.edu"> <package name="ncurses" version="5.9" /> </repository> <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed=" https://toolshed.g2.bx.psu.edu"> <package name="zlib" version="1.2.8" /> </repository> </action> <action type="shell_command">sed -i 's/-lcurses/-lncurses/' Makefile</action> <action type="shell_command">sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile< /action> <action type="shell_command">make</action> <action type="move_file"> <source>samtools</source> <destination>$INSTALL_DIR/bin</destination> </action> </actions> <action type="set_environment"> <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> <environment_variable action="set_to" name="SAMTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable> </action> </actions_group> </install> So, to me, it sounds like this is trying to compile/install a distribution meant for linux, but I'm on OSX. I was able to successfully install samtools 1.2 with no errors. Is there anyway to update, or modify the code for the BWA installation recipe to use as a dependency samtools 1.2 rather then 1.1? Or does anyone have any suggestions on how to get samtools 1.1 to work? I tried making a bin/ directory and moving a precompiled samtools binary for 1.1 in the directory. But galaxy didn't seem to recognize that the dependency was satisfied manually. Any advice would be greatly appreciated. Thank you, -Hans