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Error Codes
The {: .no_toc} statement hides a specific heading from the table of contents. However this is generally unhelpful, as table of content entries provide useful jump targets for users, especially users using screenreaders that need the landmarks to navigate around a page.
Please do not use {: .no_toc}
Embedding YouTube videos is generally discouraged as these are often less generally accessible to users. We support linking the YouTube videos from the tutorial metadata automatically via the GTN Video Library, however we want to avoid YouTube videos embedded directly in the materials as they interrupt the flow of the materials, and it is not clear for learners if the video content is mandatory or optional.
As such, by saying "no embedded videos", we ensure that the training materials have textual content for 100% of the steps required to complete a tutorial, something necessary for blind learners.
This error code is emitted when you link to the GTN via an "external" link, i.e. you've used the domain of the GTN in your link.
By using the {% link %} syntax instead, you can ensure that anyone who forks the GTN still sees a functional site that links to the correct tutorial, rather than redirecting to the main GTN.
Additionally we have automated link checking, but we only check internal links to the same site, as external links are harder to check and produce actionable intel.
DOIs used in text could be better served by the {% cite %} syntax, as we can automatically generate a nicely formatted references list. We can also compute on this list, provide it in different formats, and do more useful things with it.
Screenreader users often navigate by hyperlink, moving from one link to the next. If the text for this link is here, they will just hear "link here link here link here" which is very unhelpful for them.
Instead by providing useful link text, they can hear things like "link galaxy documentation link usegalaxy.eu link Hiltemann et al 2018"
These errors are emitted when you have a malformed Jekyll invocation. They should be {% function arguments %} and if any of the % or {/} are missing, it will not be invoked properly, and the result will not be what is expected.
We have attempted to automatically detect these issues and provide suggestions.
A citation used in the {% cite key %} command was not found. Please check that there is a matching value of key in your bibliography file.
The referenced snippet file you've used with {% snippet path/to/file.md %} does not seem to exist, please double check this.
The {% tool [Some Name](toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy9) %} syntax only expects a tool ID, e.g.
- toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy9
- upload1
Not the full URL to the server. This is because these links need to be generic for every server, and we accomplish that by only including the ID portion. Please remove any https://... portion from the tool ID to resolve this issue.
It can be that you are referencing a short tool ID, i.e. one of the ones built-in to Galaxy. If an error is generated here, this can be because we forgot to allow-list that tool ID. We may need to update the linting.
Otherwise it can be that that tool is only installed on that specific server, which is not ideal as GTN tutorials are designed to work across every server.
We have developed a new syntax for box titles that is more accessible to users using screenreaders. Please use this new syntax.
-> ### {% icon tip %} Tip: Use Galaxy!
+> <tip-title>Use Galaxy!</tip-title>The new syntax should be easier to remember and use.
Please avoid target="_blank", as it is inaccessible.
We are aware some users prefer every link to open in a new tab by default, but in the interests of accessibility, please teach those users to ctrl-click or use the right click menu.
This Bibliography file is missing one or more mandatory fields, please add them if possible.
This is a bad symlink, probably referencing a non-existent file. This can break the training materials build and cause unexpected issues.
Spaces in filenames cause issues, please remove them or replace them with - or _.
This workflow file is missing the tags field, we require that every workflow have tags indicating which topic it is related to.
This workflow file is missing the annotation field, we require that every workflow have an 'annotation' field matching the tutorial title.
A step in this tutorial uses a tool from the test toolshed, which we do not allow. Test ToolShed tools generally indicate tools that are not ready to be installed on production Galaxies, meaning that this tutorial cannot be generally useful across multiple servers, an explicit aim of ours.
Please either replace with production quality ToolShed tools (if you can use an alternative), or work with the tool developers to get the tool into the production ToolShed.
The file referenced by {% link ... %} could not be found. This can happen especially if you've got URL parameters or fragments in your link, e.g. {% link tutorial.md#introduction %} or similar.
This JSON file cannot be parsed, please check it.