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dependency_script.rst

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dependency_script command

This section is auto-generated from the help text for the planemo command dependency_script. This help message can be generated with planemo dependency_script --help.

Usage:

planemo dependency_script [OPTIONS] PROJECT

Help

Compile tool_dependencies.xml to bash script.

An experimental approach parsing tool_dependencies.xml files into bash shell scripts, intended initially for use within Continuous Integration testing setups like TravisCI.

Parses the tool_dependencies.xml files from the specified projects, and converts them into an installation bash script (dep_install.sh), and a shell script (env.sh) defining any new/edited environment variables.

These are intended to be used via bash dep_install.sh (once), and as source env.sh prior to running any of the dependencies to set the environment variable within the current shell session.

Both dep_install.sh and env.sh require $INSTALL_DIR be defined before running them, set to an existing directory with write permissions. Beware than if run on multiple tools, they can over-write each other (for example if you have packages for different versions of the same tool). In this case make separate calls to planemo dependency_script and call the scripts with different installation directories.

This command will download (and cache) any URLs specified via Galaxy download actions. This is in order to decompress them and determine the relevant sub-folder to change into as per the Tool Shed install mechanism, so that this can be recorded as a cd comand in the bash script.

The download cache used by planemo dependency_script and the resulting output script dep_install.sh defaults to ./download_cache (under the current working directory), and can be set with $DOWNLOAD_CACHE.

If the tool_dependencies.xml file includes SHA256 checksums for downloads, these will be verified after downloading to the cache (by either planemo dependency_script or bash dep_install.sh).

This is experimental, and is initially intended for use within continuous integration testing setups like TravisCI to both verify the dependency installation receipe works, and to use this to run functional tests.

Options:

-r, --recursive             Recursively perform command for nested repository
                            directories.
--fail_fast                 If multiple repositories are specified and an
                            error occurs stop immediately instead of
                            processing remaining repositories.
--download_cache DIRECTORY  Directory to cache downloaded files, default is
                            $DOWNLOAD_CACHE
--help                      Show this message and exit.