melbournebioinformatics / melbioinf_docs Goto Github PK

Guides to cover:

• brief overview (e.g. RNA-seq for DGE)
• relevant tutorials
• relevant web links to articles, other training

Hi,

I'm trying this tutorial in proteomics, but I can't view the data since it gives me this error in Galaxy:

Bad Request 

The server could not comply with the request since it is either malformed or otherwise incorrect.

Suggest linking to EMBL-ABR training database, Galaxy Training Network.

There is only one protocol, would be better to remove this section.

use:

This is not as nice as mdx.showable but that isn't working.

https://github.com/melbournebioinformatics/MelBioInf_docs/blob/master/docs/tutorials/variant_calling_galaxy_1/variant_calling_galaxy_1.md still links to https://docs.google.com/document/pub?id=1NfythYcSrkQwldGMrbHRKLRORFFn-WnBm3gOMHwIgmE - this should be turned into markdown. Are there other instances?

to get a DOI.

Remove tutorial from view if troubleshooting is needed.

Anna to ask @Slugger70

On the main page - https://www.melbournebioinformatics.org.au/tutorials/ - , the menu bar is in the top left corner (three lines, but not named). For some people this won't be obvious. See if there's a way to point to this / make more obvious.

also re: links to GTN tutorials : check these also work on Galaxy-Mel/Au

We have override styling in docs/extra.css.

The mkdocs-material theme allows us to set the main and secondary colour by setting palette in mkdocs.yml. We should consider replacing a lot of our CSS by instead setting the palette options, with the exception probably being the custom image used for the header bar to match the website.

Under "General Tutorials", make a header re: the MB clusters and link to the documentation about how to use them.

Documentation is here:
https://www.melbournebioinformatics.org.au/documentation/

I have added links to the most recent version of these, which is at Andrew Robinson's page (http://andrewjrobinson.github.io/vlsci-docs/tutorials/unix/). Our version is older.

pros: better formatting for mdx.showable; cons: LaTrobe icon is included

Our formatting for question-hint-answer does not render as nicely as mdx.showable.

Ideally we will update our version at some stage, or remove in favour of pointing to alternate courses (e.g. run by Research Platforms).

(If there are no privacy issues).
By doing this we can give it a DOI.

Check this is done automatically and if so, work out how to do systematically.