Hans, An actions tag with specified architecture and operating system will only be processed if both attributes match, so that one would not be executed on your OSX system. As regards the error in the sed command, I've created a pull request for the IUC's samtools 1.1 (and others with the same error) tool dependency definition, once that is accepted I'll be able to update the toolshed with the working code. Thank you for alerting me to that error. - Dave Bouvier http://galaxyproject.org http://usegalaxy.org On 07/09/2015 05:22 PM, Hans Vasquez-Gross wrote:

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-Linux-x86_64.tgz</action> <action type="move_directory_files"> <source_directory>.</source_directory>

<destination_directory>$INSTALL_DIR</destination_directory> </action> </actions> <actions> <package name="ncurses" version="5.9"> <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="zlib" version="1.2.8"> <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/1.1/samtools-1.1.tar.bz2</action> <action type="set_environment_for_install"> <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> <package name="ncurses" version="5.9" /> </repository> <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> <package name="zlib" version="1.2.8" /> </repository> </action> <action type="shell_command">sed -i 's/-lcurses/-lncurses/' Makefile</action> <action type="shell_command">sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$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

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