Galaxy provides a method for managing the dependencies of Galaxy tools installed from the Tool Shed. In this case, it is simply necessary to set the tool_dependency_dir option of config/galaxy.ini to a path writable by the Galaxy server.
However, some tools which have not been migrated to the Tool Shed still require manual installation of dependent binaries. In addition, administrators may choose to utilize existing versions of dependencies already installed on the system, rather than rely on versions installed from the Tool Shed. The documentation below covers these cases.
A list of dependencies for unmigrated tools can be found on the Admin/Tools/ToolDependencies page.
$PATH is the shell environment variable that instructs the shell (i.e. bash) what directories to search for binaries. Originally, Galaxy expected all binaries to be located on the $PATH set when the Galaxy server starts. This is still an acceptable method to provide dependencies to Galaxy. You can manipulate this variable as in this example:
$ echo $PATH /usr/bin:/bin:/usr/sbin:/sbin $ type bowtie bowtie not found $ export PATH="/galaxy/software/linux2.6-x86_64/bin:$PATH" $ echo $PATH /galaxy/software/linux2.6-x86_64/bin:/usr/bin:/bin:/usr/sbin:/sbin $ type bowtie bowtie is /galaxy/software/linux2.6-x86_64/bin/bowtie
Galaxy-specific environment file
The galaxy configuration file contains an option environment_setup_file that if set to the path of a file, will cause that file to be sourced prior to running a job. You may find it more convenient to persist your environment changes in this file as opposed to the user's startup files due to the complications described below.
Changes to $PATH can be persisted by setting them in your shell's startup file(s). This typically means ~/.bash_profile for bash, but please see the bash documentation on startup files or the INVOCATION section of the bash(1) man page to understand the intricacies of how that file is read. Of particular importance, if you are starting Galaxy in a method other than manual invocation from a shell prompt (with sh run.sh) such as with an init script, it is likely that your startup file will not be read. In this instance, you should set $PATH in the startup file or use.
Setting $PATH in your shell startup files may work depending on your DRM - this is how we set up the environment for the Public Galaxy Site which runs TORQUE PBS. However, this may not work for other DRMs such as Sun Grid Engine (SGE). For SGE, please see the -v and -V options to qsub and how to set these in ~/.sge_request or the job runner URL.
Managed Tool Dependencies
Individual tool configurations should contain <requirement type="package"> tags which can be used by the tool dependency system. This system works by taking the following steps:
- Create a directory accessible to Galaxy and any cluster on which Galaxy runs tools
Set tool_dependency_dir in the Galaxy config file (galaxy.ini) to the above path
Create a subdirectory of the above directory that matches the string in the <requirement> tags of tool you want to use
- Create a subdirectory of the subdirectory you just contained matching the version number of the package you have installed or are installing
Create a symbolic link from the name default to the version directory you just created (this is used for tools which have a package requirement but do not specify a version of that package; most tools behave this way). Note: default must be a sybolic link, an actual directory named default will be ignored.
- In the version subdirectory create either:
a bin/ directory or
an env.sh file as described below
For example, if the <requirement> is <requirement type="package">bowtie</requirement> and you have installed or plan to install version 0.12.7:
$ cd <tool_dependency_dir> $ mkdir bowtie $ cd bowtie $ mkdir 0.12.7 $ ln -s 0.12.7 default
Using the bin/ subdirectory
Since most *nix tools install to a bin/ subdirectory of their package root, a simple shortcut exists for installing tools directly into the tool_dependency_dir. With the bowtie example above, simply:
$ cd <tool_dependency_dir>/bowtie/0.12.7 $ mkdir bin $ cp /path/to/bowtie-0.12.7_binaries/* bin/
In this case, Galaxy will prepend <tool_dependency_dir>/bowtie/0.12.7/bin to $PATH immediately before it runs the bowtie tool.
If you prefer, you could also symlink the bin/ directory to the location of your bowtie bin directory if you already have bowtie installed elsewhere on your system, or symlink the 0.12.7 directory to the location of the real bin directory's parent directory.
Using the env.sh file
For more complete control over how the environment is configured, you can instead choose to create an env.sh file. This is a file that is sourced (not executed) by the shell to set up any appropriate environment variables needed to execute the software. In the bowtie example, this would be <tool_dependency_dir>/bowtie/0.12.7/env.sh and would look like this:
# configure PATH to bowtie binaries PATH="/path/to/bowtie-0.12.8_binaries:$PATH" export PATH
This file will then be sourced immediately before Galaxy runs the bowtie tool. More complex software may require you to set up other environment variables, and env.sh is the appropriate place to do that.