readme

CONTRIBUTING.md

@@ -60,7 +60,7 @@ conda activate metatag-dev
 5. Run tests
 
 ```bash
-(metatag-dev) python -m unittest discover tests
+(metatag-dev) bash tests/run_test.sh
 ```
 
 ## Working with GitHub branches
@@ -85,15 +85,6 @@ __IMPORTANT NOTES__:
 a) https://docs.github.com/en/get-started/getting-started-with-git/caching-your-github-credentials-in-git
 b) https://github.com/cli/cli/blob/trunk/docs/install_linux.md
 
-## Using GitHub codespaces
-
-Alternatively, you can directly work on a developer environment in the browser within GitHub's codespaces. To set this environment up:
-
-1. Fork repository and create new branch for your issue.
-
-2. Start a new Codespace for the new branch. GitHub will build an environment with all required dependencies as well as MetaTag the first time (it will take a couple of minutes). MetaTag will be installed in a conda environment named "metatag-dev".
-
-
 ## Tests on push and pull request to main
 
 MetaTag's repo contains a [GitHub Action](https://github.com/features/actions) to perform build and integration tests which is triggered automatically on push and pull request events to the main brach. Currently the tests include building and installing MetaTag in Ubuntu and running the [test](tests) suit.

README.md

@@ -14,31 +14,38 @@ This repository contains tools to assign taxonomy and function annotations to sh
 ## :wrench: Setup
 The easiest way to use MetaTag is through the provided [docker](https://www.docker.com/) container. To use it, pull the image:
 
-```
+```bash
 docker pull ghcr.io/robaina/metatag:latest
 ```
 
 Then run the container interactively:
 
-```
+```bash
 docker run -i ghcr.io/robaina/metatag:latest
 ```
 
 Otherwise, you can install MetaTag like this:
 
 1. Fork git repo into local machine (click on fork) and clone, or simply clone main branch with
-```
+```bash
 git clone https://github.com/Robaina/MetaTag.git
 ```
-2. CD to project traits and set conda environment if not already set:
-```
-conda env create -n traits -f envs/metatag.yml
+
+2. CD to project MetaTag and set conda environment if not already set:
+```bash
+conda env create -n metatag -f envs/metatag.yml
 ```
 
-## Installation test
-To check that everything is working properly, you can run a test what will perform the entire workflow on a minimal dataset. To run it, call bash script:
+3. Build and install MetaTag:
+```bash
+conda activate metatag
+(metatag) poetry build && pip install dist/metatag*.whl
 ```
-bash tests/run_test.sh
+### Installation test
+To check that everything is working properly, you can run a test what will perform the entire workflow on a minimal dataset. To run it, call bash script:
+```bash
+conda activate metatag
+(metatag) bash tests/run_test.sh
 ```
 It should produce a final tree with query sequences placed on it, as well as a bunch of intermediary files without any errors.
 
@@ -50,6 +57,12 @@ Pynteny would not work without these awesome projects:
 - [prodigal](https://github.com/hyattpd/Prodigal)
 - [pyfastx](https://github.com/lmdu/pyfastx)
 - [biopython](https://github.com/biopython/biopython)
+- [papara](https://cme.h-its.org/exelixis/web/software/papara/index.html)
+- [epa-ng](https://github.com/Pbdas/epa-ng)
+- [gappa](https://github.com/lczech/gappa)
+- [empress](https://github.com/biocore/empress)
+- [muscle](https://github.com/biocore/empress)
+- [mafft](https://github.com/biocore/empress)
 - [numpy](https://github.com/numpy/numpy)
 - [pandas](https://github.com/pandas-dev/pandas)
 - [psutil](https://github.com/giampaolo/psutil)