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tags: GeneLab
---

# Rendering markdown as pdf
>Among other places, I found this path [here](https://gist.github.com/justincbagley/ec0a6334cc86e854715e459349ab1446), and ended up finding the way below to be the easiest.

[toc]

## Install needed program in [conda](https://astrobiomike.github.io/unix/conda-intro) environment

conda create -y -n grip python=3
conda activate grip
pip install grip

Now we need the markdown file we want to turn into a pdf, **but we don't want to get the page that looks like this (if doing this to a page from github)**:

<a href="https://i.imgur.com/7it0KyI.png"><img src="https://i.imgur.com/7it0KyI.png"></a>

We want to click the "Raw" button to get to the plain text version, which will look something like this:

<a href="https://i.imgur.com/k3ne8tb.png"><img src="https://i.imgur.com/k3ne8tb.png"></a>

Then we want to get that file on our computer, so we can copy the link at the top of our browser and download it with `curl` like this example (if this particular example file still exists – if it doesn't because this is the future times, you will get a 404 error at the next step, but the process will work the same with your own):

curl -LO https://raw.githubusercontent.com/asaravia-butler/GeneLab_Data_Processing/master/Metagenomics/Illumina/GL-DPPD-7107.md

## Render local html

grip GL-DPPD-7107.md

Go to the link it prints out that it is serving it on, e.g. something like `localhost:6419/`. (I was working in a chrome browswer, so the images below match that)

> **NOTE**
> The example file used previously is gone, and was updated. So the pics below don't match the new example file above. But the concepts are the same.

## Remove anything we don't want, like the top part here
Right-click and select "Inspect":

<a href="https://i.imgur.com/7PUSI8M.png"><img src="https://i.imgur.com/7PUSI8M.png"></a>

In the top-right box, select the elements we want to remove, hovering over them highlights them in the rendered html page, e.g.:

<a href="https://i.imgur.com/AfLPWVM.png"><img src="https://i.imgur.com/AfLPWVM.png"></a>

And hitting the `delete` key on our keyboard when that object is selected deletes it from this local rendering:

<a href="https://i.imgur.com/GPRPwGH.png"><img src="https://i.imgur.com/GPRPwGH.png"></a>

Get rid of everything wanted, here I did up to the Table of Contents, so this will start as page 2 and we'll add the cover page:

<a href="https://i.imgur.com/25A8KW4.png"><img src="https://i.imgur.com/25A8KW4.png"></a>

## Saving as PDF
Then right-click and select "Print..." (I have no idea why this is the standard way to save as a PDF):

<a href="https://i.imgur.com/1xgCiRW.png"><img src="https://i.imgur.com/1xgCiRW.png"></a>

Click on the "More settings" drop-down menu and make sure "Headers and footers" box is *not* checked, and that the "Background graphics" is checked:

<a href="https://i.imgur.com/a2SwFXJ.png"><img src="https://i.imgur.com/a2SwFXJ.png"></a>

I also found a "scale" setting that sometimes helps to get more text on the page width-wise, so mess with that if things are getting cut off more than we can trim down.

Click save. The browser can now be closed and `ctrl+c` can be run on the command line to cancel the `grip` program.

## Adding front page (for GL-DPPDs)
I saved Amanda's front page word doc as a template so we can easily modify it. Can be downloaded with this line:

curl -L -o GL-protocol-pg-1-template.docx https://ndownloader.figshare.com/files/26031350

I modified that in word and saved it as a PDF. Then I combined them into one PDF. I use Mac's Preview app to do this, by dragging the cover page thumbnail over to the full PDF doc:

<a href="https://i.imgur.com/x182DJU.png"><img src="https://i.imgur.com/x182DJU.png"></a>