Galaxy Toolshed Installation


  • an Admin account on a running instance of Galaxy


Obviously, a Galaxy Toolshed installation of MiModD requires Galaxy to be installed and running, but since you are interested in this way of installing MiModD you are likely a Galaxy server administrator already. If not, we recommend you to follow the instructions in the official Galaxy docs to get your own instance up and running. Alternatively, you may follow the instructions on Galaxy Installation and Initial Configuration in this guide, but these contain some steps that are really only necessary to integrate a Standard Installation of MiModD into Galaxy.


MiModD is available from the main Galaxy Tool Shed. The installation process is basically the same as for any other Tool Shed tool, i.e., as described here.

Use the repositories

  • mimodd_main

    to install all tools except the MiModD Read Alignment and the Variant Annotation and List Installed SnpEff Genomes tools, then

  • mimodd_aln

    to install the MiModD Read Alignment tool if desired. The reason why we put this tool in a separate repository is that it can be replaced with other NGS read alignment tools - we recommend bowtie2, in particular - that you may have installed on your Galaxy instance already.

  • mimodd_snpeff

    to install the MiModD Variant Annotation and List Installed SnpEff Genomes tools. These two tools require, and enable the MiModD package to interact with, a SnpEff installation on your system.

    The iuc-managed snpeff Tool Shed repository offers very similar and compatible functionality, but has a very different concept of interacting with SnpEff. Essentially, the iuc tools treat SnpEff and its databases as a component of Galaxy, while the MiModD tools use SnpEff as a purely external tool.

    We leave it up to you, which approach you prefer for your system.


If you decide that you want to install MiModD’s full functionality, i.e., all three Tool Shed repositories above, you can, alternatively, install all of them together via the suite_mimodd repository.

After having installed the MiModD tools of your choice, stay in the Admin section of the Galaxy interface and select Manage Tool Dependencies, which should display a page similar to this one:


Check that the MiModD software package got installed alongside the MiModD Galaxy tools. In addition, make sure that your Galaxy has the requirements for uploading files and for setting external metadata installed.

If you do not see a green tickmark to the right of the

  • MiModD,
  • samtools and/or
  • bcftools

requirements highlighted in the above image, but the red not installed icon (as in the image) instead, check the corresponding Select boxes (2) & (3), click on Install checked dependencies using Conda (4) and wait for the installation process to finish.


Although MiModD will be fully usable right after the installation process finishes, for optimal performance, it is highly recommended that you configure the package.

If you do not mind restarting your Galaxy server once, your simplest option will be the environment variable-based configuration of the package.

If you want to avoid a server restart, you can configure the package from the command line by changing into the __mimodd@<installed_version> directory inside your Galaxy conda environments folder, then running:

bin/python -m MiModD.config [--parameter VALUE] ...

as explained in changing MiModD settings from the command line.

Enhancing the user experience

As a disadvantage of the Tool Shed installation scheme, the MiModD tools will be added to the Tools bar in more or less random order. With the rather big number of individual tools in the package this can be annoying, so we recommend you to edit your Galaxy’s integrated_tool_panel.xml file to sort the tools in their intended order, which can be seen here.

In addition, there is one tool, MiModD Report Variants, that produces html output, which you should exempt from Galaxy’s html filtering rules by adding the tool to the Display Whitelist.