This document summarizes any special instructions that must be followed when upgrading this tool.
NOTE: This upgrade removed Tool Shed installation support, if you had previously installed this tool from a Tool Shed please refer to the updated installation instructions in README.md.
If you had previously installed the tool manually from GitHub please follow the instructions below:
Note: We are assuming that you cloned the repo to galaxy/tools/irida-galaxy-importer.
Change the following line in galaxy/config/tool_conf.xml:
From
<tool file="irida-galaxy-importer/irida_import/irida_import.xml" />To
<tool file="irida-galaxy-importer/irida_import.xml" />Now we need to regenerate the tool XML file:
pushd galaxy/tools/irida-galaxy-importer
python -m irida_import.main --generate_xml
popdAt this point you will likely need to restart galaxy so that it can load the new tool XML.
Please ensure that you have all dependencies installed that are listed in Section 2.1.2 of the README.MD