immuneml_tools

Galaxy tool wrappers for immuneML. The tools rely on immuneML version 2.0.1 or newer.

https://immuneml.uio.no/

Installation:

The tools can be installed from a Galaxy toolshed. You can also install them offline by editing Galaxy config files in the usual way.

New datatype immuneml_receptors

No matter how you install the tools, you will need to define a new datatype, which is done as follows:

1. In your galaxy.yml look up the name of your datatypes_config_file. If the name is not yet defined, set

datatypes_config_file: datatypes_conf.xml

2. Make datatypes_conf.xml by copying datatypes_conf.xml.sample unless a datatypes_config_file was already defined.
3. Add the following line to your datatypes_config_file:

<datatype extension="immuneml_receptors" type="galaxy.datatypes.text:Html" subclass="True"/>

The line has to be inside <registration> along with the other datatypes.

The immuneML package

Conda installation of immuneML typically takes several minutes. There is general information about Galaxy dependency resolution here: https://docs.galaxyproject.org/en/release_20.05/admin/conda_faq.html