Revert "update note about jaxlib"

README.md

@@ -13,28 +13,8 @@ LocalColabFold is an installer script designed to make ColabFold functionality a
 - **No GPU limitations**
 - **NOT necessary to prepare the large database required for native AlphaFold2**.
 
-## Note (Jun 16, 2022)
-
-ColabFold now depends on [JAX](https://github.com/google/jax) == 0.3.13 and jaxlib > 0.3.7, so you may encounter this error message after updating your localcolabfold using `./update_linux.sh`:
-
-```
-  File "/path/to/colabfold_batch/colabfold-conda/lib/python3.7/site-packages/jax/_src/lib/__init__.py", line 91, in check_jaxlib_version
-    raise RuntimeError(msg)
-RuntimeError: jaxlib is version 0.1.72, but this version of jax requires version >= 0.3.7.
-```
-
-To fix this issue, please upgrade your jax and jaxlib:
-
-```bash
-# '/path/to/your/colabfold_batch' should be substituted to your path, e.g. '/home/moriwaki/Desktop/colabfold_batch'
-# install GPU-supported jaxlib
-/path/to/your/colabfold_batch/colabfold-conda/bin/python3.7 -m pip install https://storage.googleapis.com/jax-releases/cuda11/jaxlib-0.3.10+cuda11.cudnn82-cp37-none-manylinux2014_x86_64.whl
-/path/to/your/colabfold_batch/colabfold-conda/bin/python3.7 -m pip install jax==0.3.13
-```
-
 ## New Updates
 
-- 16Jun2022, version 1.4.0 released. See [Release v1.4.0](https://github.com/YoshitakaMo/localcolabfold/releases/tag/v1.4.0)
 - 07May2022, **Updated `update_linux.sh`.** See also [How to update](#how-to-update). Please use a new option `--use-gpu-relax` if GPU relaxation is required (recommended).
 - 12Apr2022, version 1.3.0 released. See [Release v1.3.0](https://github.com/YoshitakaMo/localcolabfold/releases/tag/v1.3.0)
 - 09Dec2021, version 1.2.0-beta released. easy-to-use updater scripts added. See [How to update](#how-to-update).

README_ja.md

@@ -4,7 +4,6 @@
 
 ## アップデート情報
 
-- 2022年6月16日, version 1.4.0 リリース。[Release v1.4.0](https://github.com/YoshitakaMo/localcolabfold/releases/tag/v1.4.0)
 - 2021年12月9日, β版。簡単に使えるアップデートスクリプトを追加。[アップデートのやり方](#アップデートのやり方)を参照。
 - 2021年12月4日, LocalColabFoldは最新版の[pipでインストール可能なColabFold](https://github.com/sokrypton/ColabFold#running-locally)に対応しました。このリポジトリではrelax（構造最適化）処理を行うために必要な他のパラメータファイルとともにColabFoldをインストールするためのスクリプトを提供しています。AlphaFoldとAlphaFold-Multimerの重みパラメータは初回の実行時に自動的にダウンロードされます。
 

install_colabbatch_M1mac.sh

@@ -48,14 +48,17 @@ rm openmm.patch
 wget -qnc https://raw.githubusercontent.com/YoshitakaMo/localcolabfold/main/update_M1mac.sh --no-check-certificate
 chmod +x update_M1mac.sh
 # install ColabFold and Jaxlib
-colabfold-conda/bin/python3.8 -m pip install https://files.pythonhosted.org/packages/bd/57/88cea9e14dacaea82ca86fac2bf6ecb8b7fd99622d776e4131786ce5b65e/tensorflow_macos-2.7.0-cp38-cp38-macosx_11_0_arm64.whl
+colabfold-conda/bin/python3.8 -m pip install tensorflow-macos
 colabfold-conda/bin/python3.8 -m pip install git+https://github.com/deepmind/tree.git
 colabfold-conda/bin/python3.8 -m pip install git+https://github.com/google/ml_collections.git
-colabfold-conda/bin/python3.8 -m pip install dm-haiku appdirs pandas absl-py docker
+colabfold-conda/bin/python3.8 -m pip install dm-haiku==0.0.4 appdirs pandas absl-py==0.13.0 docker
 colabfold-conda/bin/python3.8 -m pip install alphafold-colabfold --no-deps --no-color
 colabfold-conda/bin/python3.8 -m pip install "colabfold[alphafold] @ git+https://github.com/sokrypton/ColabFold" --no-deps --no-color
-colabfold-conda/bin/python3.8 -m pip install jaxlib==0.3.10 --no-deps --no-color
-colabfold-conda/bin/python3.8 -m pip install jax==0.3.13 chex scipy toolz --no-deps --no-color
+colabfold-conda/bin/python3.8 -m pip install jax==0.2.25 --no-deps --no-color
+colabfold-conda/bin/python3.8 -m pip install jaxlib==0.1.74 -f "https://dfm.io/custom-wheels/jaxlib/index.html" --no-deps --no-color
+colabfold-conda/bin/python3.8 -m pip install numpy==1.21.1 --no-deps --no-color
+colabfold-conda/bin/python3.8 -m pip install chex --no-deps --no-color
+colabfold-conda/bin/python3.8 -m pip install scipy --no-deps --no-color
 
 # bin directory to run
 mkdir -p $COLABFOLDDIR/bin

install_colabbatch_intelmac.sh

@@ -48,8 +48,8 @@ wget -qnc https://raw.githubusercontent.com/YoshitakaMo/localcolabfold/main/upda
 chmod +x update_intelmac.sh
 # install ColabFold and Jaxlib
 colabfold-conda/bin/python3.7 -m pip install "colabfold[alphafold] @ git+https://github.com/sokrypton/ColabFold"
-colabfold-conda/bin/python3.7 -m pip install https://storage.googleapis.com/jax-releases/mac/jaxlib-0.3.10-cp37-none-macosx_10_9_x86_64.whl
-colabfold-conda/bin/python3.7 -m pip install jax==0.3.13
+colabfold-conda/bin/python3.7 -m pip install https://storage.googleapis.com/jax-releases/mac/jaxlib-0.1.74-cp37-none-macosx_10_9_x86_64.whl
+colabfold-conda/bin/python3.7 -m pip install jax==0.2.25
 
 # bin directory to run
 mkdir -p $COLABFOLDDIR/bin

install_colabbatch_linux.sh

@@ -29,8 +29,9 @@ chmod +x update_linux.sh
 conda install -c conda-forge -c bioconda kalign3=3.2.2 hhsuite=3.3.0 -y
 # install ColabFold and Jaxlib
 colabfold-conda/bin/python3.7 -m pip install "colabfold[alphafold] @ git+https://github.com/sokrypton/ColabFold"
-colabfold-conda/bin/python3.7 -m pip install https://storage.googleapis.com/jax-releases/cuda11/jaxlib-0.3.10+cuda11.cudnn82-cp37-none-manylinux2014_x86_64.whl
-colabfold-conda/bin/python3.7 -m pip install jax==0.3.13
+colabfold-conda/bin/python3.7 -m pip install https://storage.googleapis.com/jax-releases/cuda111/jaxlib-0.1.72+cuda111-cp37-none-manylinux2010_x86_64.whl
+colabfold-conda/bin/python3.7 -m pip install jax==0.2.25
+
 # bin directory to run
 mkdir -p $COLABFOLDDIR/bin
 cd $COLABFOLDDIR/bin
@@ -48,6 +49,9 @@ chmod +x colabfold_batch
 # hack to share the parameter files in a workstation.
 cd ${COLABFOLDDIR}/colabfold-conda/lib/python3.7/site-packages/colabfold
 sed -i -e "s#props_path = \"stereo_chemical_props.txt\"#props_path = \"${COLABFOLDDIR}/stereo_chemical_props.txt\"#" batch.py
+# Use gpu-accelerated relaxation.
+cd ${COLABFOLDDIR}/colabfold-conda/lib/python3.7/site-packages/alphafold/relax
+sed -i -e 's/CPU/CUDA/g' amber_minimize.py
 # Use 'Agg' for non-GUI backend
 cd ${COLABFOLDDIR}/colabfold-conda/lib/python3.7/site-packages/colabfold
 sed -i -e "s#from matplotlib import pyplot as plt#import matplotlib\nmatplotlib.use('Agg')\nimport matplotlib.pyplot as plt#g" plot.py