In. Cred. Ible. Content. Much thanks, will cite.

Dead link tho:

"anvi-summarize
[...]
The result of anvi-summarize is a static HTML output you can browse in your browser, send to your colleagues, put it on your web page (an example from one of our papers is here)**, or attach it to your submission as a supplementary data for review. When you run anvi-summarize,"

'Omics terms can be difficult to learn. Having them described in a single page may help new comers to overcome this barrier quickly and transfer knowhow that may be a pain to transfer through more formal means. But developing a vocabulary is indeed a challenge, and certainly requires input from the community that uses these terms.

To address these issues, @ivagljiva and I have started a vocabulary page here:

https://anvio.org/vocabulary/

Now it is mature enough to ask for your help if you are interested in contributing to it. So the purpose of this issue is to detail how one can contribute to 'omics vocabulary.

Once you do it, you will be eligible to get some stickers from us by filling out this simple form:

https://forms.gle/kQTCysGDMtXe16AZ8

Yes, we certainly are in the territory of quid pro quo, and we are proud of it. Thank you in advance for playing and considering to contribute!

What is this, a vocabulary for ants?

Yes, well, no, it is not for ants, but we do know it is indeed very tiny. That's why we decided to open it to the community so it can grow, and we look forward to your input to improve it. For instance, here is an incomplete list of terms that could benefited from definitions by you:

• single-copy core gene (now addressed by @karkman in #4)
• virome (now addressed by @simroux in #5)
• hidden markov model (now addressed by @thapasz in #6)
• community (now addressed by @xvazquezc in #7)
• microbiome, microbiota (now addresed by @xvazquezc in #8)
• tree of life, de novo assembly, de bruijn graph (now addressed by @crusher083 in #9)
• single-amplified genome (SAG), metabolomics, metabolite (now addressed by @crusher083 in #13)
• metaproteomics, strain, haplotype, orthologous genes, paralogous genes (now addressed by @crusher083 in #14).

Fine, I'll contribute. But how can I do it?

🎊

You can contribute by adding and defining new terms, or improve existing definitions. From a technical point, contributing is straightforward and can be done in multiple ways.

First, please read through the vocabulary page to have an idea of its language and approach to definitions. Once you know what you want to add to the vocabulary, or improve existing definitions, naturally you will want to edit the page. The content behind the vocabulary page is here:

https://github.com/merenlab/anvio.org/blob/main/vocabulary/index.md

Which means, this is the actual source file that is rendered and displayed at https://anvio.org/vocabulary/, and it is the file the contents of which must be updated. There are two ways to make a contribution: (1) send us a pull request (which is our preferred way), or (2) send us a comment. Both options are are detailed below. For the first one you will need a GitHub account. For the second one you will simply need git installed on your system (if you have anvi'o installed on your computer, you have git installed on it, too).

Send a pull request

The best way is to prepare a "Pull Request" for the GitHub repository, because it will forever associate your changes with your username. For this you will need to,

• 'Fork' the repository at https://github.com/merenlab/anvio.org to your own GitHub account,
• Edit the file at vocabulary/index.md,
• Commit your changes with the mentioning of this call which will automatically happen if you simply put this anywhere in the title or text:#3),
• And send a Pull Request.

This is a very standard workflow on GitHub, and there is a lot of resources online like this one to learn how to craft and send a pull request. While I know it sounds boring and difficult if you don't already know it, learning this is a great way to get your foot in the door to make more contributions to open-source projects, and understand the power of version tracking.

Send your changes as a comment

If you don't want to deal with pull requests and all, you still can make a contribution very easily.

Go to your terminal, and type these commands to get a copy of the anvi'o web repository:

mkdir -p ~/github/
cd ~/github/
git clone https://github.com/merenlab/anvio.org.git

Then open this file in your text editor (perhaps something like Atom or MacDown, and certainly not Word or anything like Microsoft Word or TextEdit):

~/github/anvio.org/vocabulary/index.md

Once you are done with your edits, save your changes, and in your terminal type these commands:

cd ~/github/anvio.org/
git diff vocabulary/index.md

Copy the entire output, and come back to this issue, and paste it as a comment with a small description of what you have done. If you copy-paste this and then replace the text with your output, it will even look good:

``` diff
YOUR OUTPUT GOES HERE
```

What happens after I contribute?

If your contribution gets into the vocabulary page, we will ask you to go fill out this form. After which we will send you a sticker, and list your name on the vocabulary page 😇

Thank you very much for your help in advance.

WAIT, I have more questions!

Of course you do!

How much contribution is enough?

ANY contribution is. Anything you change and ends up on the page, is a contribution. We of course would like to see new terms, better definitions, etc, but you can also play the system for stickers.

So I can make as many tiny contributions as I want and get so many stickers?

To conserve energy, we only promise to send one sticker per contribution, and no more than 4 letters to the same address :) Do whatever you wish to do with this EXTREMELY KEY information :p After 4, we will send our thanks. Virtually.

Who decides whether a contribution ends up on the page or not?

Since someone has to take this responsibility on themselves, Meren will do it for now and forever unless someone else wants to do it.

Hi there.

I Just found out that on the Anvi'o User Tutorial for Metagenomic Workflow
the link that should point out an example of anvi-summarize command, leads to a page not found message.

Here is the sentence in case it helps:
"an example from one of our papers is here"

cc @ahenoch

The following detects shell to enable the path setting + update to work in zsh. It also uses the current working directory, fixing issues for any folks who don't place the anvio directory in ~/github

mkdir -p "${CONDA_PREFIX}/etc/conda/activate.d/"
SHELL_NAME=$(basename "$SHELL")

# Define color/formatting codes for different shells
if [ "$SHELL_NAME" = "zsh" ]; then
  # Zsh shell
  blue_text=$(tput setaf 4)
  red_text=$(tput setaf 1)
  reset_text=$(tput sgr0)
else
  # Bash shell (default to original formatting)
  blue_text="\033[1;34m"
  red_text="\033[0;31m"
  reset_text="\033[0m"
fi

# Create the activation script
cat <<EOF >"${CONDA_PREFIX}/etc/conda/activate.d/anvio.sh"
# creating an activation script for the conda environment for anvi'o
# development branch so (1) Python knows where to find anvi'o libraries,
# (2) the shell knows where to find anvi'o programs, and (3) every time
# the environment is activated, it synchronizes with the latest code from
# the active GitHub repository:
export PYTHONPATH=\$PYTHONPATH:${PWD}
export PATH=\$PATH:${PWD}/bin:${PWD}/sandbox
echo -e "${blue_text}Updating from anvi'o GitHub ${red_text}(press CTRL+C to cancel)${reset_text} ..."
cd ${PWD} && git pull && cd -
EOF

Tested for zsh on M2 mac, please do test on bash. This might be worth obscuring as a script.

A simpler solution might be to enable pip install -e . :)

(edited. had a pythonpath error initially :)

Hi Anvi'o team,

Just a quick note that on the installation page at the end of 4.3 Troubleshooting, the "... anvi'o resources here ..." link leads to a page not found. Otherwise, the site is looking really nice! Thanks for all of the hard work and awesome tools...as always!

Cheers,
Chris