Ag3.x data access guide

malariagen / vector-data

Documentation, discussion forum and issue tracker for malaria vector genomic data released by MalariaGEN.

https://malariagen.github.io/vector-data/

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Ag3.x data access guide #55

Closed ahernank closed 11 months ago

ahernank commented 1 year ago

Include a single page that describes both the data cloud access and the downloads for Ag3.1

Note:

We still need to update malariagen_data to include the 3.1 release.
I have used wget and gsutil commands here to be consistent with the other guides in vector-data but in the PUG we use curl commands instead.
It would be good to link the study website page (when it is live) to this access guide.

For my local setup to work, I had to modify the environment to include:

jsonschema>=3 (this is included in the requirements to deploy but I also required it to solve the initial environment)
pip install nbconvert==5.6.1 (issue described here but solved by downgrading the version)
pip install jinja2==3.0.3 (issue described here)

As these seem to be local requirements, I have not changed any of the environment configurations to include these.

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ahernank commented 1 year ago

cc @alimanfoo, @leehart

ahernank commented 1 year ago

This is the same version we looked at together a while ago, where we deprecate the analysis NBs in favour of the training course website examples.

@leehart @alimanfoo @cclarkson It would be great to know if you have any comments on the Ag3.1 Data Access guide here, as this will serve as template for the other .x release pages.

After these, I can include the rest of the guides on this PR, and then deal with Af on a separate one, as we currently do not have any Af references at all the user guide.

ahernank commented 12 months ago

Updated with the comments from our meeting, please let me know if there any other suggestions.

@leehart, I've also linked the new API docs to simplify the API section on the docs, please let me know if you'd like any changes here.

alimanfoo commented 11 months ago

Hi @ahernank, just had a quick scan and noticed there is an ag3/ag3.0 page in the TOC but I didn't see a corresponding notebook file? Did I miss something?

ahernank commented 11 months ago

Thanks @alimanfoo, sorry. Fixed now, this file was just renamed from intro to ag3.0 to avoid confusion.

ahernank commented 11 months ago

I'll be merging this one shortly, unless there are any concerns but will keep an eye in case we need any edits after deploying the new version.