galaxy/doc/source/admin/dependency_resolvers.rst

.. _dependency_resolvers:


Dependency Resolvers in Galaxy
==============================

There are two parts to building a link between Galaxy and command line bioinformatics tools: (1) the tool XML that
specifies a mapping between the Galaxy web user interface and the tool command line, and (2) the actual command-line
tools, known as Galaxy *tool dependencies*, which must be installed and available on the system(s) where Galaxy is
configured to run those tools. The job script that Galaxy uses to run a job includes commands (such as changes to the
``PATH`` environment variable) that are generated by *dependency resolvers*. These same dependency resolvers are used by
the Galaxy administrative UI to display whether an installed tool's dependencies have been installed on the Galaxy
server, and to show how they will be resolved at job runtime.  There is a default dependency resolver configuration but
administrators can provide their own configuration using the ``dependency_resolvers`` configuration option in Galaxy's
configuration file, ``galaxy.yml``. Previously this configuration was stored in a separate XML file,
``dependency_resolvers_conf.xml``. Loading the dependency resolvers configuration from that XML file is deprecated but
still supported, however, the documentation and sample configuration file for the XML format can only be found in Galaxy
releases prior to 21.09.

.. note::

    The *tool XML* referred to below is different from the deprecated *dependency resolvers XML* referred to above.

The binding between tool XML and the command-line tools they need to run is specified in the tool XML using
``<requirement>`` tags, for example:

.. code-block:: xml

    <requirement type="package" version="0.7.10.039ea20639">bwa</requirement>

In some cases these requirement tags can be specified without a version:

.. code-block:: xml

    <requirement type="package">bedtools</requirement>

These declared requirements are passed as inputs to the dependency resolver in order to generate the environmental setup
in the job script so that the correct tool dependencies required by the tool are found on the ``$PATH``.

Default Dependency Resolvers
----------------------------

The default configuration of dependency resolvers is equivalent to the following configuration in ``galaxy.yml``:

.. code-block:: yaml

    galaxy:
      dependency_resolvers:
        - type: tool_shed_packages
        - type: galaxy_packages
        - type: conda
        - type: galaxy_packages
          versionless: true
        - type: conda
          versionless: true

This default dependency resolver configuration contains five items:

1. First, the *Tool Shed packages dependency resolver* is used, which resolves packages installed from the Galaxy Tool
   Shed using legacy ``tool_dependencies.xml`` files,
2. then the *Galaxy packages dependency resolver* is checked for a package matching the requirement name and version,
3. then the *Conda dependency resolver* is checked for a package matching the requirement name and version. If no
   versioned match can be found, it then moves on to searching for unversioned matches, that is,
4. the *Galaxy packages dependency resolver* is checked for a package matching the required name only, and
5. finally the *Conda dependency resolver* is checked for a package matching the required name only.

If any of the dependency resolvers succeed, a dependency resolution object is returned and no more resolvers are
called. This dependency resolution object provides shell commands to prepend to the shell script that runs the
command-line tool.

This order can be thought of as a descending order of deliberation. Tool Shed dependencies must be declared next to the
tool by the tool author and must be selected for installation at tool installation time - this requires specific actions
by both the tool author and the deployer who installed the tools. The dependency is therefore highly
crafted to the individual tool. If Galaxy packages have been setup, the deployer of a Galaxy tool has purposely crafted
tool dependency statements for a specific installation - this is slightly less deliberate than tool shed packages but
such requirements are less likely to be incidentally resolved than Conda packages. Conda recipes are neither tied to
tools or a specific installation and are maintained in Conda channels such as Bioconda.

So while tool shed packages are first - they are also somewhat deprecated. Maintaining Conda recipes makes it easier
to describe software dependencies both inside of Galaxy and outside.

Tool Shed Dependency Resolver
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. code-block:: yaml

    - type: tool_shed_packages

The ``tool_shed_packages`` dependency resolver works with explicit software packages installed from the Galaxy Tool
Shed as described by legacy ``tool_dependencies.xml`` files. When such a package is installed from the Tool Shed it
creates a directory structure under the directory that is specified as the ``tool_dependency_dir`` in Galaxy's
configuration. This directory structure contains references to the tool's ID, owner (in the Tool Shed) and version
string (amongst other things) and ultimately contains a file named ``env.sh`` that contains commands to make the
dependency runnable. This ``env.sh`` file is installed, along with the packaged tool, by the tool package and doesn't
require any configuration by the Galaxy administrator. The Tool Shed-specific components of the path come from
Galaxy's install database (see the ``install_database_connection`` option in the Galaxy configuration) and are not
configured by hand.

All new and updated tools in the Tool Shed that follow `Galaxy IUC <https://galaxyproject.org/iuc/>`_ best practices
no longer use Tool Shed dependencies, and must have dependencies resolvable via Conda. Because of this, the Tool Shed
resolver is largely only relevant to older Galaxy servers that have old tools installed.

The Tool Shed dependency resolver is not able to resolve package requirements that do not have a version string,
like the ``bedtools`` example above.

Galaxy Packages Dependency Resolver
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. code-block:: yaml

    - type: galaxy_packages
      versionless: <true|false>
      base_path: <filesystem path>

The ``galaxy_packages`` dependency resolver allows Galaxy admins to specify how Galaxy should load manually
installed packages.

This resolver can be configured with the following parameters, all of which are optional:

base_path
    The path under which the resolver looks for packages matching the tool's specified requirements. The default value
    is the value of the ``tool_dependency_dir`` option in Galaxy's configuration file.

versionless
    Ignore requirement versions and use the "default" version instead (see below).

Below the base path, the Galaxy Packages resolver looks for a directory matching the requirement name, e.g.
``bedtools``. Inside the name directory, the resolver looks for a directory matching the requirement version. For
example, if the Galaxy tool specifies that it needs ``bedtools`` version 2.20.1, the dependency resolver will look for
a directory ``<base_path>/bedtools/2.20.1``.

If the Galaxy Package dependency resolver finds a ``bin`` directory in this directory, it adds it to the ``PATH``
used by the scripts Galaxy uses to run tools. If, however, it finds an ``env.sh`` script, it sources this
script before running the tool that requires this dependency. This can be used to set up the environment
needed for the tool to run.

A simple example might be to assume that a collection of bioinformatics software is manually installed in various
directories under ``/opt/biosoftware``. In this case a ``<tool_dependency_dir>/bedtools/2.20.1/env.sh`` could be
setup to add the corresponding bedtools installation to the Galaxy tool execution's ``PATH``.

.. code-block:: bash

    #!/bin/sh

    export PATH=$PATH:/opt/biosoftware/bedtools/2.20.1/bin


As another example, this ``env.sh`` uses `Environment Modules <http://modules.sourceforge.net/>`_
to setup the environment for ``bedtools``

.. code-block:: bash

    #!/bin/sh

    if [ -z "$MODULEPATH" ] ; then
      . /etc/profile.d/module.sh
    fi

    module add bedtools/bedtools-2.20.1

The Galaxy Package dependency resolver operates quite similarly when used in versionless mode. Instead of looking
for a directory named after a version, it looks for a directory symbolic link named ``default`` that links to a
concrete version such as the ``2.20.1`` example above. For example if ``bedtools/default`` links to ``bedtools/2.20.1``.
It then looks for a `bin` subdirectory or ``env.sh`` and incorporates these in the tool script that finally gets run.
This versionless (i.e. default) lookup is also used if the package requirement does not specify a version string.

Conda Dependency Resolver
~~~~~~~~~~~~~~~~~~~~~~~~~

.. code-block:: yaml

    - type: conda
      versionless: <true|false>
      prefix: <filesystem path>
      exec: <filesystem path>
      debug: <true|false>
      ensure_channels: [channel, channel...]
      auto_install: <true|false>
      auto_init: <true|false>
      copy_dependencies: <true|false>
      read_only: <true|false>

The ``conda`` dependency resolver is used to find (and optionally install-on-demand) dependencies using the `Conda
Package Manager <https://conda.io/>`__.  For a very detailed discussion of Conda dependency resolution, check out the
:doc:`Conda FAQ <conda_faq>`.

Additionally, the conda resolver makes use of *mulled* dependencies, where all of the tool's specified requirements
are installed into a single Conda environment. More details about mulled dependencies can be found in the
:doc:`Mulled Containers <special_topics/mulled_containers>` documentation.

This resolver can be configured with the following parameters, all of which are optional:

prefix
    The root of the conda installation used to locate dependencies in (default: value of global ``conda_prefix``
    option or ``<tool_dependency_dir>/_conda`` otherwise).

exec
    The conda executable to use, it will default to the one on ``$PATH`` (if available) and then to
    ``<conda_prefix>/bin/conda``.

versionless
    Whether to resolve tools using a version string or not (default: ``false``).

debug
    Pass debug flag to conda commands (default: ``false``).

ensure_channels
    Conda channels to enable by default. See https://conda.io/docs/user-guide/tasks/manage-channels.html for more
    information about channels. This defaults to the value of the global ``conda_ensure_channels`` option or
    ``conda-forge,bioconda`` otherwise.  This order should be consistent with the `Bioconda prescribed
    order <https://github.com/bioconda/bioconda-recipes/blob/master/config.yml>`__ if it includes ``bioconda``.

auto_install
    If ``true``, Galaxy will look for and install missing tool dependencies before running a job (default: value of
    the global ``conda_auto_install`` option or ``false`` otherwise).

auto_init
    If ``true``, Galaxy will try to install Conda from the web automatically if it cannot find a local copy and
    ``conda_exec`` is not configured (default: the value of the global ``conda_auto_init`` option or ``true``
    otherwise).

copy_dependencies
    If ``true``, Galaxy will copy dependencies over instead of symbolically linking them when creating per-job
    environments. This is deprecated because Conda will do this as needed for newer versions of Conda - such as the
    versions targeted with Galaxy 17.01 and later.

read_only
    If ``true``, Galaxy will not attempt to install or uninstall requirement sets into this environment.

The conda resolver will search for Conda environments named::

    __<requirement_name>@<requirement_version>

in the case that a tool only has one requirement tag, or::

    mulled-v1-<hash>

when a tool has multiple requirement tags, where ``<hash>`` is a hash derived from the requirements' names and
versions.

For example, to try an administrator-maintained read-only Conda installation at ``/hpc/conda`` first and then a
Galaxy-maintained writable Conda installation at ``/galaxy/conda`` second (where any missing dependencies will
be automatically installed at tool runtime), use the following:

.. code-block:: yaml

    - type: conda
      auto_init: false
      auto_install: false
      prefix: /hpc/conda
    - type: conda
      auto_init: true
      auto_install: true
      prefix: /galaxy/conda

Lmod Dependency Resolver
~~~~~~~~~~~~~~~~~~~~~~~~

.. code-block:: yaml

    - type: lmod
      versionless: <true|false>
      lmodexec: <filesystem path>
      settargexec: <filesystem path>
      modulepath: <filesystem path[:filesystem path:...]>
      mapping_files: <filesystem path>
      skip_availability_check: <true|false>


The ``lmod`` dependency resolver interacts with the `Lmod environment modules system <https://lmod.readthedocs.io/>`__
commonly found on HPC systems.

This resolver can be configured with the following parameters, all of which are optional:

lmodexec
    Path to the Lmod executable on your system. This cannot be just "module" because module is actually a bash
    function and not the real Lmod binary (see the result of the "type module" command). Default: value of the
    ``$LMOD_CMD`` environment variable.

settargexec
    Path to the settarg executable on your system. Default: value of the ``$LMOD_SETTARG_CMD`` environment variable.

modulepath
    Path to the folder that contains the LMOD module files on your system. This can be a single path or a
    semicolon-separated list of paths. Default: value of the ``$MODULEPATH`` environment variable.

versionless
    Set to ``true`` to resolve a dependency based on its name only (the version number is ignored). Only modules
    marked as Default will be listed by the "avail" command (The -d option is used). Default: ``false``.

mapping_files
    Path to a YAML configuration file that can be used to link tools requirements with existing Lmod modules. Default:
    ``config/lmod_modules_mapping.yml``

skip_availability_check
    Set to ``true`` to skip filtering module dependencies using ``module avail`` and attempt to load each
    module listed in the depedencies (default: ``false``).
    This setting should be used when during dependency resolution modules are not listed in ``module avail``,
    but can be expected to be present when using ``module load`` in the job script,  such as child modules
    in hierarchical module systems. Note: the order in which dependencies are listed could be important.

Environment Modules Dependency Resolver
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. code-block:: yaml

    - type: modules
      versionless: <true|false>
      modulecmd: <filesystem path>
      modulepath: <filesystem path[:filesystem path:...]>
      find_by: <directory|avail>
      prefetch: <true|false>
      default_indicator: <string>
      skip_availability_check: <true|false>


The ``modules`` dependency resolver interacts with the `Environment Modules system <https://modules.sourceforge.net/>`__
commonly found on HPC systems.

This resolver can be configured with the following parameters, all of which are optional:

modulecmd
    Path to Environment Modules' ``modulecmd`` tool.

modulepath
    Value used for ``$MODULEPATH`` environment variable, used to locate modules.

versionless
    Whether to resolve tools using a version string or not (default: ``false``).

find_by
    Whether to use the ``DirectoryModuleChecker`` or ``AvailModuleChecker`` (permissable values are ``directory`` or ``avail``,
    default is ``avail``).

prefetch
    In the AvailModuleChecker, prefetch module info with ``module avail`` (default: ``true``).

default_indicator
    What indicates to the AvailModuleChecker that a module is the default version (default: ``(default)``). Note
    that the first module found is considered the default when no version is used by the resolver, so
    the sort order of modules matters.

skip_availability_check
    Set to ``true`` to skip filtering module dependencies using ``module avail`` and attempt to load each
    module listed in the depedencies (default: ``false``).
    This setting should be used when during dependency resolution modules are not listed in ``module avail``,
    but can be expected to be present when using ``module load`` in the job script,  such as child modules
    in hierarchical module systems. Note: the order in which dependencies are listed could be important.

The Environment Modules dependency resolver can work in two modes. The ``AvailModuleChecker`` searches the results
of the ``module avail`` command for the name of the dependency. If it is configured in versionless mode,
or is looking for a package with no version specified, it accepts any module whose name matches and is a bare word
or the first module whose name matched. For this reason, the default version of the module should be the first one
listed, something that can be achieved by tagging it with a word that appears first in sort order, for example the
string ``(default)`` (yielding a module name like ``bedtools/(default)``). So when looking for ``bedtools`` in
versionless mode the search would match the first module called ``bedtools``, and in versioned mode the search would
only match if a module named ``bedtools/2.20.1`` was present (assuming you're looking for ``bedtools/2.20.1``).

The``DirectoryModuleChecker`` looks for files or directories in the path specified by ``MODULEPATH`` or
``MODULESHOME`` that match the dependency being resolved. In versionless mode a match on simply
the dependency name is needed, and in versioned mode a match on the dependency name and
version string is needed.

If a module matches the dependency is found, code to executed ``modulecmd sh load`` with the name of the dependency
is added to the script that is run to run the tool. E.g. ``modulecmd sh load bedtools``. If version strings are being
used, they'll be used in the ``load`` command e.g. ``modulecmd sh load bwa/0.7.10.039ea20639``.


Homebrew Dependency Resolver
~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The ``homebrew`` dependency resolver uses the `Homebrew Package Manager <https://brew.sh/>`__ to resolve requirements.
It is highly experimental, undocumented, and unmaintained, and likely to be dropped from the code base.


Brewed Tool Shed Package Resolver
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The ``brewed_tool_shed`` dependency resolver was an attmept to resolve tool shed packages that had been auto converted
to the tool shed. It is highly experimental, undocumented, unmaintained, and will almost certainly be removed from the
code base.