From 6166cdc03cb35acb23815aab7aeb749c213c6d8a Mon Sep 17 00:00:00 2001
From: Fortune Iriaye <firiaye@uab.edu>
Date: Thu, 19 Dec 2024 11:44:52 -0600
Subject: [PATCH] Update README.md
---
README.md | 29 +++++++++++++++++------------
1 file changed, 17 insertions(+), 12 deletions(-)
diff --git a/README.md b/README.md
index 9b0db93..7acc8c2 100644
--- a/README.md
+++ b/README.md
@@ -1,26 +1,31 @@
# Using this container on Cheaha
-You will need to follow these instructions:
+Please follow these instructions to set up for Alphafold3 on Cheaha.
-1. If you already cloned the Alphafold3 [github repo](https://github.com/google-deepmind/alphafold3), you do not need to clone this repo. But if you have not, you can clone this gitlab repo.
-1. Download the needed databases for Alphafold3 by running the command. Make sure you are in the same folder as the `fetch_databases.sh` file before running the below command, or use the absolute file path to run it.
+1. Pull this container using the command:
``` bash
-
- ./fetch_databases.sh <DB_DIR> #<DB_DIR> is your preferred location for storing the databases
-
+ singularity pull alphafold3.sif docker://gitlab.rc.uab.edu:4567/rc-data-science/community-containers/alphafold3/alphafold3:<tag>
+
+ #get the tag by clicking on "Deploy" -> "Container Registry" -> Click on "alphafold3/alphafold3" and then use the "Copy image path" option to get the image path used above, complete with the appropriate tag (latest).
```
-1. Now pull the container with singularity using
- ``` bash
+1. If you already cloned the Alphafold3 [github repo](https://github.com/google-deepmind/alphafold3), you do not need to clone this repo, otherwise clone this repo.
- singularity pull alphafold3.sif docker://gitlab.rc.uab.edu:4567/rc-data-science/community-containers/alphafold3/alphafold3:<tag>
+1. Download the needed databases for Alphafold3 by running the below command. Make sure you are in the same folder as the `fetch_databases.sh` file before running the below command, or use an absolute path for the file to run it.
+ ``` bash
+ ./fetch_databases.sh <DB_DIR> #<DB_DIR> is your preferred location for storing the databases
```
-1. When the above step is completed, you can now run the Alphafold3 container on Cheaha using the command to test it out.
+You will also need to get the model parameters for alphafold3, you have to fill out a form, and submit a request to Google.
- ``` bash
+1. When the above steps are completed, run the Alphafold3 container on Cheaha to test it out using the commands:
+ ``` bash
singularity exec --nv alphafold3.sif sh -c 'nvidia-smi'
+ ```
+ or
- ```
\ No newline at end of file
+ ``` bash
+ singularity exec --nv alphafold3.sif python3 /app/run_alphafold.py --help
+ ```
--
GitLab