Step 2: Generating the AXIOME Control File
A description of the pipeline is kept within an AXIOME control file (with .ax extension). This file allows a user to recreate an entire analysis automatically. It is created using the axiome ui command. Before you proceed into the AXIOME UI, take note of the locations of the file mapping and metadata mapping files created in the previous step.
The UI is terminal-based. This means that it can be run in an ssh session. To launch the UI, use the command axiome ui.
To navigate the UI, use the arrow keys to move between elements on the screen. ENTER will select buttons and enable checkboxes. SPACE will toggle checkboxes. If you ever get stuck and the arrow keys are not moving you, pressing TAB will move you to the next element.
Pressing ENTER at the splash screen will move you to the next screen.
On the Select Workflow page, you can select different default workflows. This will automatically check the appropriate steps on the following page (Select Pipeline Steps). Currently, the only option is "Default", which gives a good set of default steps for a QIIME run.
The next page is where the method for each step of the pipeline is chosen. It can span multiple pages, which can be navigated to by pressing the Down arrow at the bottom of the page. The current page is indicated in the bottom right corner.
There are two types of controls. If the boxes are round "(X)", then only one option can be selected. If the boxes are square "[X]", then multiple options can be selected. To deselect an option in a square bracket, press the Space bar.
The titles of each step can be selected with the Enter key. This brings up a message that describes the step and each of the options available in that step.
When you press Next, it will validate the file mapping page. If there are any errors in the format, it will not let you proceed.
Each step may have a configuration page that allows the user to enter in any required details. Where possible, default values will be filled in for you.
For example, the Mapping step requires that a mapping file be copied over from a source. The only requirement here is the absolute filepath of your metadata mapping file (created in Step One). Tip: The text boxes for filepaths support tab-completion (though a bug prevents long filepaths from being displayed properly).
Some of the configuration steps may require you to know the filepaths of certain reference files. Be sure to know where to find your sequence reference OTUs and taxonomy (ie. GreenGenes or SILVA data) and your alignment template (core_set_aligned.fasta.imputed from GreenGenes).
Some configuration pages have the options to "Add Copy of Submodule". This will create a new copy of that step as the next page. For example, if you are running a PCoA analysis, adding a copy of the submodule will allow you to set one to unweighted UniFrac, and the next to weighted UniFrac. "Remove Copy of Submodule" will delete that submodule so that it is no longer run.
All of the options you have configured will be stored in a .ax extension file. This will allow you to load it later on and change options with the axiome ui -i <filename>.ax command.
On the save screen, fill out the absolute filepath of the desired file location. Pressing Tab when it is blank will automatically fill in the present working directory. Pressing Save will save the file at the desired location, and allow you to exit.
- The .ax file is an XML formatted file. You can edit it in a text editor to change any arguments if you wish to avoid the UI.
- The analyses prefixed with MESaS are scripts that are available at the MESaS GitHub page.