From d9213b7facaea9b943c33f3f61c64c917e73d6ce Mon Sep 17 00:00:00 2001
From: Cameron Hyde <chyde@neoformit.com>
Date: Tue, 29 Oct 2024 10:38:49 +1000
Subject: [PATCH] Document alphafold outputs.py

---
 tools/alphafold/README.md                  |  8 ++++++-
 tools/alphafold/scripts/pip_install_jax.sh | 26 ----------------------
 tools/alphafold/scripts/requirements.txt   | 20 +++++++++++++++++
 3 files changed, 27 insertions(+), 27 deletions(-)
 delete mode 100755 tools/alphafold/scripts/pip_install_jax.sh
 create mode 100644 tools/alphafold/scripts/requirements.txt

diff --git a/tools/alphafold/README.md b/tools/alphafold/README.md
index 46c0efe2..061898a3 100644
--- a/tools/alphafold/README.md
+++ b/tools/alphafold/README.md
@@ -25,7 +25,13 @@ When you `planemo test` the wrapper should use the mock AlphaFold run, which cop
 
 ## Generating additional outputs
 
-The `./scripts/outputs.py` script is used to generate additional outputs from an AF2 run. This script is complex because it must handle all different output variations (monomer, multimer, N models, etc.). The test script `tests/test_outputs.sh` runs a basic end-to-end test with the sample outputs available in `test-data`. Each of these directories is a complete output directory for an AF2 run, for each of the three model presets:
+To run the outputs.py file you will need to install some dependencies (a virtual environment is highly recommended):
+
+```sh
+pip install -r scripts/requirements.txt
+```
+
+The `./scripts/outputs.py` script is used to generate additional outputs from an AF2 run. This script is complex because it must handle all different output variations (monomer, multimer, N models, etc.). The test script `tests/test_outputs.sh` runs a basic end-to-end test with the sample outputs available in `test-data/`. Each of these directories is a complete output directory for an AF2 run, for each of the three model presets:
 
 ```
 test-data
diff --git a/tools/alphafold/scripts/pip_install_jax.sh b/tools/alphafold/scripts/pip_install_jax.sh
deleted file mode 100755
index deb97edf..00000000
--- a/tools/alphafold/scripts/pip_install_jax.sh
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/usr/bin/env bash
-
-# python3.8
-
-JAX=0.3.25
-JAXLIB=0.3.25+cuda11.cudnn805
-
-cat <<EOF >> /tmp/requirements.txt
-absl-py==1.0.0
-biopython==1.79
-chex==0.0.7
-dm-haiku==0.0.9
-dm-tree==0.1.6
-docker==5.0.0
-immutabledict==2.0.0
-jax==0.3.25
-ml-collections==0.1.0
-numpy==1.21.6
-pandas==1.3.4
-scipy==1.7.2
-tensorflow-cpu==2.11.0
-matplotlib==3.8.*
-EOF
-
-pip install -r /tmp/requirements.txt
-pip install jax==${JAX} jaxlib==$JAXLIB -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
diff --git a/tools/alphafold/scripts/requirements.txt b/tools/alphafold/scripts/requirements.txt
new file mode 100644
index 00000000..743dc58b
--- /dev/null
+++ b/tools/alphafold/scripts/requirements.txt
@@ -0,0 +1,20 @@
+# tested on python3.8 + 3.10
+
+absl-py==1.0.0
+biopython==1.79
+chex==0.0.7
+dm-haiku==0.0.9
+dm-tree==0.1.6
+docker==5.0.0
+immutabledict==2.0.0
+jax==0.3.25
+ml-collections==0.1.0
+numpy==1.21.6
+pandas==1.3.4
+scipy==1.7.2
+tensorflow-cpu==2.11.0
+matplotlib==3.8.*
+
+-f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
+jax==0.3.25
+jaxlib==0.3.25+cuda11.cudnn805