Querying tool information¶
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:
^= 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
--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
This is a new version of the
list_tools which replaces the
list_installed_tools command (which is no longer
--mode=tools option replicates the output
from the old
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 https://toolshed.g2.bx.psu.edu):
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
- 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 \ https://testtoolshed.g2.bx.psu.edu/view/devteam/trimmer/dec27ea206c3 \ --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
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.
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
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
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
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/* \ --remove_from_disk
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:
toolshed.g2.bx.psu.edu 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 https://palfinder.ls.manchester.ac.uk --mode=export > palfinder.tsv nebulizer install_tool http://127.0.0.1 --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.