From 6fe995bc0b1fce812744521c23ddce3baa60b2cd Mon Sep 17 00:00:00 2001
From: Will Nickols <78048944+WillNickols@users.noreply.github.com>
Date: Thu, 7 Dec 2023 10:58:31 -0500
Subject: [PATCH] Update README.md

---
 README.md | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/README.md b/README.md
index ab3ef27..ec2328f 100644
--- a/README.md
+++ b/README.md
@@ -10,20 +10,12 @@ git clone https://github.com/WillNickols/assembly_workflow
 cd assembly_workflow
 conda env create -f assembly_environment.yml
 conda activate biobakery_assembly
-git clone --recursive https://github.com/chklovski/checkm2.git
-checkm2/bin/checkm2 database --download --path databases/checkm/
+checkm2 database --download --path databases/checkm/
 export CHECKM_DATA_PATH=$(pwd)/databases/checkm/
 mkdir tmp_to_delete && mkdir -p databases/phylophlan && touch tmp_to_delete/tmp.fa && phylophlan_metagenomic -d SGB.Jul20 --database_folder databases/phylophlan/ -i tmp_to_delete/; rm -r tmp_to_delete/
 export PHYLOPHLAN_PATH=$(pwd)/databases/phylophlan/
 ```
 
-Run the following commands to install the necessary R packages.
-```
-R
-install.packages(c("docopt", "dplyr", "data.table", "stringr", "doParallel", "tidyr"))
-q()
-```
-
 Once the conda environment is created and you are in the `assembly_workflow` directory, you can activate the environment with these commands:
 ```
 conda activate biobakery_assembly