List of software tools found within planned or released plugins?

Because ghost-tree is dependent on FastTree, MUSCLE and Sumaclust, I have been trying to find which plugins these software tools are found in. I see Fasttree is in “qiime phylogeny fasttree”… it would be nice to have a better way to find them since FastTree isn’t mentioned in the qiime2 dev spreadsheet. This one was obvious, but perhaps MUSCLE is found somewhere else, it’d be nice to have a better search option or something.

Are MUSCLE and Sumaclust planned? If not, what is the best approach for me to take. Do I want to have the ghost-tree plugin install these tools, or build separate plugins that ghost-tree is dependent on?


Hey @Jennifer_Fouquier,
These external programs aren’t really part of the plugins, they’re just called by the plugins. For example, see where we call FastTree in the q2-phylogeny plugin.

For your ghost-tree plugin, you’d want to do this same thing - just call the external programs as we’re doing in the fasttree method of the q2-phylogeny plugin. When you package your plugin for distribution on conda (we can help you with this part when the time comes) you would include these external programs as dependencies in the conda recipe. You can search Anaconda to figure out where/if those binaries are available through conda.

We will ultimately have a plugin registry that may include information about external programs that are required by a plugin, but you wouldn’t need that for what you’re doing here. On a related note, we do now have a page that lists the “core distribution” plugins and their methods.

Hope this helps!