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README.md

How to run a copy of this website locally

You can run a local version of this website to see how your changes will look like when they are pushed. For this, you need to install jekyll, which can be doen the following way on a Mac OSX:

sudo gem install jekyll

If the command gem is not found, or your Ruby version is outdated, try to install it the following way first:

brew install ruby

Once the installation is complete, you can get a copy of the web site from GitHub:

git clone https://github.com/merenlab/web.git
cd web

To make sure you have the necesary gems, run:

bundle install

And run the following command in this directory:

bundle exec jekyll serve --incremental

You should see a similar output in your terminal:

Configuration file: /Users/evan/Software/web/_config.yml
Configuration file: /Users/evan/Software/web/_config.yml
            Source: /Users/evan/Software/web
       Destination: /Users/evan/Software/web/_site
 Incremental build: enabled
      Generating...
                    done in 6.585 seconds.
 Auto-regeneration: enabled for '/Users/evan/Software/web'
Configuration file: /Users/evan/Software/web/_config.yml
    Server address: http://127.0.0.1:4000/
  Server running... press ctrl-c to stop.

This basically runs a local server for you to see the changes you've made locally. You can access to this server by visiting the URL http://127.0.0.1:4000/ with your browser.

With the --incremental flag every change you will make in any of the files will be reflected to your local website automatically.

If you are not seeing some of the changes you expect to see, press ctrl-c to stop the server on your termianl, clean out the static web directory by running the command rm -rf _site/, and re-run the server using the command above.

How to get yourself fired from the lab

It is simple.

You can make the following changes in the web site:

find ./_posts/ -type f | xargs sed -i '' -e  "s/An anvi'o/A microbial dark matter \(MDM\)/g"
find ./_posts/ -type f | xargs sed -i '' -e  "s/an anvi'o/a microbial dark matter \(MDM\)/g"
find ./_posts/ -type f | xargs sed -i '' -e  "s/Anvi'o/Microbial dark matter \(MDM\)/g"
find ./_posts/ -type f | xargs sed -i '' -e  "s/anvi'o/microbial dark matter \(MDM\)/g"
find ./_posts/ -type f | xargs sed -i '' -e  "s/anvi'o/microbial dark matter \(MDM\)/g"
find ./_posts/ -type f | xargs sed -i '' -e  "s/anvi'server/MDM'server/g"

And commit them to the main repository after making sure they look alright in your local copy:

git add .
git commit -m "name upgrade"
git push origin master

Congratulations!

Notes

If you want to show/hide content, you can use this notation in your markdown files:

<details markdown="1"><summary>Show/Hide SOME CONTENT</summary>

SOME CONTENT GOES HERE

</details>

If you want to show summary sections with a different background color, you can use this notation:

<div class="extra-info" markdown="1">

<span class="extra-info-header">Smart title for extra info</span>

EXTRA INFO GOES HERE

</div>

You should feel free to use warning and notice statements:

{:.warning}
A warning messages goes here.

{:.notice}
A notice statement goes here.
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