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Bioconductor / BioC2020

BioC2020: Where Software and Biology Connect
http://bioc2020.bioconductor.org/
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include html file #83

Closed LiNk-NY closed 4 years ago

LiNk-NY commented 4 years ago

Hi Mikhail, @mdozmorov It looks like the page renders better with the .html product rather than the .md file for some reason. Would this work for you?

cc: @mtmorgan Best, Marcel

lpantano commented 4 years ago

I can see the page nicely render.

lpantano commented 4 years ago

@mdozmorov, let me know if now this looks good and the other PR are not longer needed.

mdozmorov commented 4 years ago

It looks good. It seems impossible to make the HTML version to render within the frame and keep the menu at right, but it is better than the hand-coded Markdown tables.

@lpantano, please, merge the #82 pull request - it has Erica's changes, and I recompiled the HTML workshop page to have AMARETTO and alevin workshops.

After this merge, the following can be closed: #78 pull request, issues #81 and #76

LiNk-NY commented 4 years ago

I'm not sure how to include this <header> part of the webpage. Any ideas?

mdozmorov commented 4 years ago

Not sure either. But it looks OK as an important stand-alone page. And, it is easy to click the "back" button to get to the main web site. Will keep an eye on potential solutions.

LiNk-NY commented 4 years ago

Hi Mikhail, @mdozmorov I've re-directed the output to md instead of HTML. This works better with the way the website is rendering. See the changes that I pushed to the main branch. https://github.com/Bioconductor/BioC2020/commit/3fb03e5b2ed4a8e13475371d6d695b876c15ebca

Thanks.

mdozmorov commented 4 years ago

Thank you, Marcel, looks great! I wasn't familiar with "output: github_document". The solution to append header lines after knitting to .md works reliably.

Strangely, the output does not render workshops that lack the DESCRIPTION file. It was working previously, outputting the footnotes. Now, I can see the code for it is there, but the tables don't have footnotes. Like, for the 200 packages, those are not outputted:

    "radio1988/oneStopRNAseqWorkshop",
    "hukai916/IntegratedChIPseqWorkshop",
    "aedin/Frontiers_Supplement",

@LiNk-NY Marcel, can you check if this is a quick fix? Thanks, Mikhail

LiNk-NY commented 4 years ago

Hi Mikhail, @mdozmorov I've fixed this with the latest push to the repository. I had to add the footnotes manually since we are using "markdown" output instead of "html" from knitr::kable. Thanks!

mdozmorov commented 4 years ago

Interesting, making HTML tags in code works. The page looks complete now, I'll send a note on Slack for workshop contributors to check. Thanks, Marcel! Mikhail