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Rearrange readme
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Rich Posert committed Feb 17, 2021
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Expand Up @@ -8,24 +8,22 @@ data using ggplot in R. Options to copy a manual file for plot tweaking are
available.

## Installation
For a local user installation:
1. Clone this repo
2. run `python3 -m virtualenv venv`
3. run `venv/Scripts/activate` or `source venv/Scripts/activate`
4. run `python -m pip install -r requirements.txt`
5. Create the file `subcommands/config.py` (see `example_config.py` for help) and
add the password for your server's couchdb installation.

You're ready to go!

Setting up the server side is easy too!
### Server installation
1. Install docker
2. Create a docker-compose file from the template (change the username and password!)
3. Create an appia `config.py` from `subcommands/example_config.pyt`
4. Set the host in `subcommands/config.py` to `couchdb` and update the username
and password
5. Run `docker-compose up`

### Local/processing-only installation:
1. Clone this repo
2. Run `python3 -m virtualenv venv`
3. Run `venv/Scripts/activate` or `source venv/Scripts/activate`
4. Run `python -m pip install -r requirements.txt`
5. Create the file `subcommands/config.py` (see `example_config.py` for help) and
add the host/username/password for your server's couchdb installation (if using).

## HPLC Processing
Appia reads `.arw` or `.asc` files (from Waters and Shimadzu HPLCs, respectively)
for information about the sample and how it was run, then optionally collects all the indicated
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