From 44a158b5fd074dcfa24d9354c06766045fdb92f2 Mon Sep 17 00:00:00 2001
From: James Abbott <j.abbott@dundee.ac.uk>
Date: Sun, 18 Jun 2023 14:09:23 +0100
Subject: [PATCH] Package version tweaks to match alphafold docs as closely as
 possible and resolve alphafold3_multimer_v3 model producing NA co-ordinates

---
 colabfold_batch.yaml | 18 +++++++++++++-----
 setup.sh             |  2 +-
 2 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/colabfold_batch.yaml b/colabfold_batch.yaml
index ce7915a..17540b8 100755
--- a/colabfold_batch.yaml
+++ b/colabfold_batch.yaml
@@ -12,14 +12,22 @@ dependencies:
   - bioconda::kalign2=2.04
   - bioconda::hhsuite=3.3.0
   - bioconda::mmseqs2=14.7e284
-  - conda-forge::jax=0.4.10
-  - conda-forge::jaxlib=0.4.10=cuda*
-  - conda-forge::chex=0.1.7
-  - nvidia::cuda-nvcc=12.1.105
+  - conda-forge::jax=0.3.25
+  - conda-forge::jaxlib=0.3.25=cuda*
+  - conda-forge::chex=0.0.7
+  - nvidia::cuda-nvcc=11.4.152
   - conda-forge::biopython=1.79
+  - conda-forge::immutabledict=2.0.0
+  - conda-forge::absl-py=1.0.0
+  - conda-forge::numpy=1.22.*
+  - conda-forge::pandas=1.3.4
+  - conda-forge::scipy=1.7.3
   - conda-forge::git
   - conda-forge::curl
   - pip:
     - nvidia-cudnn-cu11==8.8.*
-    - tensorflow==2.12.*
+    - tensorflow==2.12.0
+    - ml-collections==0.1.0
+    - dm-haiku==0.0.9
+    - dm-tree==0.1.6
     - colabfold[alphafold-minus-jax]@git+https://github.com/sokrypton/ColabFold.git@v1.5.2
diff --git a/setup.sh b/setup.sh
index 32939d7..2c6db73 100755
--- a/setup.sh
+++ b/setup.sh
@@ -22,7 +22,7 @@ else
 
 	# If installation is run on a non-gpu host, some cpu-centric packages will be installed instead
 	# of cuda packages. This can be fixed with the 'CONDA_OVERRIDE_CUDA' variabe...
-	CONDA_OVERRIDE_CUDA="11.8" $CONDA env create -f colabfold_batch.yaml
+	CONDA_OVERRIDE_CUDA="11.4" $CONDA env create -f colabfold_batch.yaml
 
 	source $(dirname $CONDA_EXE)/activate colabfold_batch