Update conda yml

README.md

@@ -4,13 +4,15 @@
 
 * Clone the repo `git clone https://github.com/heathcliff233/Dense-Homolog-Retrieval.git`
 * Go to the directory `cd Dense-Homolog-Retrieval`
-* Build using requirements.txt   `conda create --name fastMSA --file requirements.txt -c pytorch -c conda-forge -c bioconda`
+* Build using environment.yml   `conda create --name fastMSA --file environment.yml -c pytorch -c conda-forge -c bioconda`
 * Activate the environment `conda activate fastMSA`
 * Get the customized Phylopandas for fasta processing `git clone https://github.com/heathcliff233/phylopandas.git`
 
 
 Please download the checkpoints [here](https://drive.google.com/file/d/1t7R_ZQJTIsFM0JVVuY9cLLa9EE2QlIVg/view?usp=sharing) and unzip. We will denote the absolute path to the checkpoint as `$MODEL_PATH`
 
+If you would like a quick test with pre-built index or want to use esm1, please switch to v1 branch.
+
 ## Offline Embedding (optional)
 * Get the path to sequence database as `$SEQDB_PATH` (require fasta format) and path to output as $OUTPUT_PATH
 * Use `python3 do_embedding.py trainer.ur90_path=$SEQDB_PATH model.ckpt_path=$MODEL_PATH hydra.run.dir=$OUTPUT_PATH` to do embedding. Please note that `$SEQDB_PATH` needs to be an absolute path.