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Remove wget from the README and clarify how to run the system.

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PiperOrigin-RevId: 289630974
This commit is contained in:
Augustin Zidek
2020-01-14 13:16:33 +00:00
committed by Diego de Las Casas
parent d8d6d1e75a
commit 32abf74fd5
2 changed files with 8 additions and 12 deletions
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alphafold_casp13/README.md
+7 -12
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@@ -34,6 +34,10 @@ pip install wheel
pip install -r alphafold_casp13/requirements.txt pip install -r alphafold_casp13/requirements.txt
``` ```
Alternatively, you can just use the `run_eval.sh` script provided which runs
these commands for you, see the section on running the system below for more
details.
## Data ## Data
While the code is licensed under the Apache License, the AlphaFold weights and While the code is licensed under the Apache License, the AlphaFold weights and
@@ -54,12 +58,7 @@ Once you have obtained access, you can download the data from
The dataset to reproduce AlphaFold's CASP13 results can be downloaded from The dataset to reproduce AlphaFold's CASP13 results can be downloaded from
[Google Cloud Storage](https://console.cloud.google.com/storage/browser/alphafold_casp13_data). [Google Cloud Storage](https://console.cloud.google.com/storage/browser/alphafold_casp13_data).
The dataset is in a file called `casp13_data.zip` which has about **43.5 GB**.
Download it e.g. using `wget` (the file is about 43.5 GB):
```shell
wget https://storage.googleapis.com/alphafold_casp13_data/casp13_data.zip
```
The zip file contains 1 directory for each CASP13 target and a `LICENSE.md` The zip file contains 1 directory for each CASP13 target and a `LICENSE.md`
file. Each target directory contains the following files: file. Each target directory contains the following files:
@@ -86,12 +85,8 @@ targets to get the contact map.
The model checkpoints can be downloaded from The model checkpoints can be downloaded from
[Google Cloud Storage](https://console.cloud.google.com/storage/browser/alphafold_casp13_data). [Google Cloud Storage](https://console.cloud.google.com/storage/browser/alphafold_casp13_data).
The model checkpoints are in a file called `alphafold_casp13_weights.zip` which
Download them e.g. using `wget` (the file is about 210 MB): has about **210 MB**.
```shell
wget https://storage.googleapis.com/alphafold_casp13_data/alphafold_casp13_weights.zip
```
The zip file contains: The zip file contains:
alphafold_casp13/run_eval.sh
+1
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@@ -27,6 +27,7 @@ TARGET_PATH="alphafold_casp13/${TARGET}" # Path to the directory with the targe
# Set up the virtual environment and install dependencies. # Set up the virtual environment and install dependencies.
python3 -m venv alphafold_venv python3 -m venv alphafold_venv
source alphafold_venv/bin/activate source alphafold_venv/bin/activate
pip install wheel
pip install -r alphafold_casp13/requirements.txt pip install -r alphafold_casp13/requirements.txt
# Create the output directory. # Create the output directory.