Managing Tools

Querying tool information

By default, list_tools displays information on all the tool repositories that are installed in a Galaxy instance:

nebulizer list_tools GALAXY

For each installed repository the details include: repository name, toolshed, owner, revision id and changeset, and installation status.

Repository details are also preceeded by a single-character ‘status’ indicator:

  • D = deprecated;
  • ^ = newer revision is also installed;
  • u = update (newer revision) is available but not installed;
  • U = upgrade available (new revision with a change of tool version) but not installed;
  • * = latest revision installed

list_tools supports a number of options to modify its behaviour, including:

  • --updateable: only list tool repositories that have uninstalled available updates or upgrades
  • --built-ins: include details of the “built-in” tools within the Galaxy instance (i.e. those not installed from a toolshed)

An alternative ‘tool-centric’ view of the tools in a Galaxy instance can be obtained using the --mode=tools option.


This is a new version of the list_tools which replaces the old list_installed_tools command (which is no longer available). The --mode=tools option replicates the output from the old list_tools command.

list_tool_panel displays information on the tool panel sections in a Galaxy instance:

nebulizer list_tool_panel GALAXY

New tool panel sections can be created when installing tool repositories.

Install, update and remove tools

install_tool installs tools from a Galaxy toolshed (by default the main Galaxy toolshed at

nebulizer install_tool GALAXY TOOL_REPOSITORY

The tool repository can be specified as:

  • [TOOLSHED] OWNER/TOOLNAME [ REVISION ] e.g. devteam/fastqc (defaults to most recent revision from the main toolshed), or devteam/fastqc e7b2202befea (specifies revision e7b2202befea)
  • toolshed URL with or without a revision (e.g.
  • --tool-panel-section: specify a tool panel section to install the tools from the repository into (otherwise tools appear at the “top level” of the tool panel)

For example: to install the most recent FastQC tool from the main Galaxy toolshed under the NGS: QC and manipulation section of the tool panel:

nebulizer install_tool GALAXY devteam/fastqc \
   --tool-panel-section="NGS: QC and manipulation"

To install a specific revision of the Trimmer tool from the test toolshed:

nebulizer install_tool GALAXY \ \
   --tool-panel-section="Test tools"

update_tool installs the latest revision of a previously installed tool repository, if a new version is available:

nebulizer update_tool GALAXY TOOL_REPOSITORY

The tool repository is specified as with install_tool except that a revision cannot be included. For example:

nebulizer update_tool GALAXY devteam/fastqc

It is also possible to include glob-style wildcards in the tool repository name and/or owner e.g. devteam/* or bgruening/deeptools_*. To request update of all tools:

nebulizer update_tool GALAXY '*/*'


update_tool doesn’t uninstall the older versions of the tools that are updated.


By default checks on the availability of updates for tools performed by the list_tools and update_tool commands are done using information cached by the Galaxy instance in question. As a result these commands may not always indicate when updates are available.

To force these commands to check the installed revisions against those in the toolshed, add the --check-toolshed option. Note however that this can impose a significant overhead which can make the commands much slower.

uninstall_tool removes a previously installed tool:

nebulizer uninstall_tool GALAXY TOOL_REPOSITORY

The tool repository is specified as with install_tool, for example to uninstall and deactivate a specific revision of a tool:

nebulizer uninstall_tool GALAXY devteam/fastqc/e7b2202befea

To uninstall all installed revisions of a tool and remove from disk:

nebulizer uninstall_tool localhost devteam/fastqc/* \

Searching for tool repositories on a Toolshed

search_toolshed searches for tools on a toolshed:

nebulizer search_toolshed QUERY

QUERY can include glob-style wildcards. For example, to search the main toolshed for Deeptools related tools:

nebulizer search_toolshed "deeptools_*"
  • --toolshed: specify the URL of the toolshed to search.

Bulk tool repository management

install_tool --file installs the tool repositories listed in a tab-delimited file into a Galaxy instance:

nebulizer install_tool GALAXY TOOLS_FILE

TOOLS_FILE must be a tab-delimited list of repositories, one repository per line in the format:


For example:        devteam bowtie_wrappers 9ca609a2a421    NGS: Mapping

list_tools --mode=export can generate a list of tool repositories already installed in a Galaxy instance in this format, e.g.:

nebulizer list_tools GALAXY --mode=export

By combining these two commands it is possible to ‘clone’ the installed tools from one Galaxy instance into another.

For example to replicate the tools installed on the ‘Palfinder’ instance into a local Galaxy:

nebulizer list_tools --mode=export > palfinder.tsv
nebulizer install_tool --file palfinder.tsv


Bulk installation of tools in this manner should be used with caution, especially when installing into a Galaxy instance which already has installed tools.