From b17aaf1821901e2dab45f9f69e4480bd0da6fb66 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Mon, 11 Dec 2023 11:06:41 +1000 Subject: [PATCH] README: Streamline, improve. --- README.md | 23 ++++++----------------- 1 file changed, 6 insertions(+), 17 deletions(-) diff --git a/README.md b/README.md index 127d25a7..c8391c44 100644 --- a/README.md +++ b/README.md @@ -57,7 +57,12 @@ conda env create -n aviary -f aviary.yml conda activate aviary pip install -e . ``` +The `aviary` executable can then be run from any directory. Since the code in +this directory is then used for running, any updates made there will be +immediately available. We recommend this mode for developing and debugging +aviary. +## Checking installation Whatever option you choose, running `aviary --help` should return the following output: @@ -86,22 +91,6 @@ Utility modules: ``` -Upon first running aviary you will be prompted to input the location for where you would like -your conda environments to be stored, the GTDB release installed on your system, the location of your -EnrichM database, and the location of your BUSCO database. These locations will be stored as environment -variables, but for aviary to be able to use those environment variables you will have to either source your .bashrc -or reactivate your conda environment depending on whether you installed aviary within a conda environment or not: - -``` -conda deactivate; conda activate aviary - -OR - -source ~/.bashrc -``` - -These environment variables can be reset using `aviary configure` - ## Databases Aviary uses programs which require access to locally stored databases. @@ -111,7 +100,7 @@ The **required** databases are as follows: * [GTDB](https://gtdb.ecogenomic.org/downloads) * [EggNog](https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.8#setup) * [CheckM2](https://github.com/chklovski/CheckM2) - +* [SingleM](https://wwood.github.io/singlem/) ### Installing databases