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Update Tensorflow docs to reflect change in version #47

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Update Tensorflow docs to reflect change in version #47

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b3be94b
Updating trRosetta application compiliation instructions.
vmullig Jun 8, 2021
774684a
Updating auto-generated documentation.
vmullig Jun 8, 2021
092778f
Updating docs that refer to Tensorflow version.
vmullig Jun 8, 2021
10a0ebb
Merge remote-tracking branch 'origin/master' into vmullig/update_tens…
vmullig Jun 9, 2021
4fbc39e
Adding version information to docs.
vmullig Jun 9, 2021
6eafa50
Updating messages.
vmullig Jun 9, 2021
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16 changes: 8 additions & 8 deletions application_documentation/trRosetta/trRosetta.md
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Expand Up @@ -10,14 +10,14 @@ The trRosetta application uses the trRosetta neural network described in Yang _e

### Compilation requirements

The trRosetta application requires that Rosetta be linked against the Tensorflow C-API libraries. To compile with Tensorflow support:

1. Download the Tensorflow 1.15 precompiled libraries for your operating system from one of the following. (Note that GPU versions require CUDA drivers; see https://www.tensorflow.org/install/lang_c for more information.)
* Linux/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-linux-x86_64-1.15.0.tar.gz
* Linux/GPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-gpu-linux-x86_64-1.15.0.tar.gz
* Windows/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-windows-x86_64-1.15.0.zip
* Windows/GPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-gpu-windows-x86_64-1.15.0.zip
* MacOS/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-darwin-x86_64-1.15.0.tar.gz
The trRosetta application requires that Rosetta be linked against the Tensorflow 2 C-API libraries, version 2.5.0 or higher. To compile with Tensorflow support:

1. Download the Tensorflow 2.5.0 precompiled libraries for your operating system from one of the following. (Note that GPU versions require CUDA drivers; see https://www.tensorflow.org/install/lang_c for more information.)
* Linux/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-linux-x86_64-2.5.0.tar.gz
* Linux/GPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-gpu-linux-x86_64-2.5.0.tar.gz
* Windows/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-windows-x86_64-2.5.0.zip
* Windows/GPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-gpu-windows-x86_64-2.5.0.zip
* MacOS/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-darwin-x86_64-2.5.0.tar.gz
* MacOS/GPU: None available.

2. Unzip/untar the archive into a suitable directory (~/mydir/ is used here as an example), and add the following environment variables:
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14 changes: 7 additions & 7 deletions ...on/RosettaScripts/xsd/constraint_generator_trRosettaConstraintGenerator_type.md
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Expand Up @@ -5,14 +5,14 @@ _Autogenerated Tag Syntax Documentation:_
---
The trRosettaConstraintGenerator takes as input a file containing a multiple sequence alignment, feeds this to the trRosetta neural network, and uses the output to generate distance and angle constraints between pairs of residues as described in Yang et al. (2020) Improved protein structure prediction using predicted interresidue orientations. Proc. Natl. Acad. Sci. USA 117(3):1496-503. https://doi.org/10.1073/pnas.1914677117.

The trRosettaConstraintGenerator requires compilation with Tensorflow support. To compile with Tensorflow support:
The trRosettaConstraintGenerator requires compilation with Tensorflow 2 support (version 2.5.0 or higher). To compile with Tensorflow support:

1. Download the Tensorflow 1.15 precompiled libraries for your operating system from one of the following. (Note that GPU versions require CUDA drivers; see https://www.tensorflow.org/install/lang_c for more information.)
Linux/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-linux-x86_64-1.15.0.tar.gz
Linux/GPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-gpu-linux-x86_64-1.15.0.tar.gz
Windows/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-windows-x86_64-1.15.0.zip
Windows/GPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-gpu-windows-x86_64-1.15.0.zip
MacOS/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-darwin-x86_64-1.15.0.tar.gz
1. Download the Tensorflow 2.5.0 precompiled libraries for your operating system from one of the following. (Note that GPU versions require CUDA drivers; see https://www.tensorflow.org/install/lang_c for more information.)
Linux/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-linux-x86_64-2.5.0.tar.gz
Linux/GPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-gpu-linux-x86_64-2.5.0.tar.gz
Windows/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-windows-x86_64-2.5.0.zip
Windows/GPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-gpu-windows-x86_64-2.5.0.zip
MacOS/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-darwin-x86_64-2.5.0.tar.gz
MacOS/GPU: None available.

2. Unzip/untar the archive into a suitable directory (~/mydir/ is used here as an example), and add the following environment variables:
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2 changes: 1 addition & 1 deletion scripting_documentation/RosettaScripts/xsd/filter_FragmentScoreFilter_type.md
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Expand Up @@ -13,7 +13,7 @@ Filter based on any score that can be calculated in fragment_picker.
outputs_name="(pose &string;)" csblast="(&string;)"
blast_pgp="(&string;)" placeholder_seqs="(&string;)"
sparks-x="(&string;)" sparks-x_query="(&string;)" psipred="(&string;)"
vall_path="(/scratch/benchmark/W.hojo-1/rosetta.Hojo-1/master/main/database//sampling/vall.jul19.2011.gz &string;)"
vall_path="(/home/vmulligan/rosetta_devcopy_local2/Rosetta/main/database//sampling/vall.jul19.2011.gz &string;)"
frags_scoring_config="(&string;)" n_frags="(200 &non_negative_integer;)"
n_candidates="(1000 &non_negative_integer;)"
print_to_pdb="(false &xs:boolean;)"
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14 changes: 7 additions & 7 deletions scripting_documentation/RosettaScripts/xsd/mover_trRosettaProtocol_type.md
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Expand Up @@ -5,14 +5,14 @@ _Autogenerated Tag Syntax Documentation:_
---
Implements the full trRosetta protocol, as described in Yang et al. (2020) Improved protein structure prediction using predicted interresidue orientations. Proc. Natl. Acad. Sci. USA 117(3):1496-503. https://doi.org/10.1073/pnas.1914677117. This mover takes as input a multiple sequence alignment, runs the trRosetta neural network, generates distance and angle constraints between pairs of residues, and carries out energy-minimization to produce a structure. Note that this mover deletes and replaces the input structure. If a native structure is provided, the mover tags the output structure with the RMSD to native.

The trRosettaProtocol mover requires compilation with Tensorflow support. To compile with Tensorflow support:
The trRosettaProtocol mover requires compilation with Tensorflow 2 support (version 2.5.0 or higher). To compile with Tensorflow support:

1. Download the Tensorflow 1.15 precompiled libraries for your operating system from one of the following. (Note that GPU versions require CUDA drivers; see https://www.tensorflow.org/install/lang_c for more information.)
Linux/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-linux-x86_64-1.15.0.tar.gz
Linux/GPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-gpu-linux-x86_64-1.15.0.tar.gz
Windows/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-windows-x86_64-1.15.0.zip
Windows/GPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-gpu-windows-x86_64-1.15.0.zip
MacOS/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-darwin-x86_64-1.15.0.tar.gz
1. Download the Tensorflow 2.5.0 precompiled libraries for your operating system from one of the following. (Note that GPU versions require CUDA drivers; see https://www.tensorflow.org/install/lang_c for more information.)
Linux/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-linux-x86_64-2.5.0.tar.gz
Linux/GPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-gpu-linux-x86_64-2.5.0.tar.gz
Windows/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-windows-x86_64-2.5.0.zip
Windows/GPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-gpu-windows-x86_64-2.5.0.zip
MacOS/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-darwin-x86_64-2.5.0.tar.gz
MacOS/GPU: None available.

2. Unzip/untar the archive into a suitable directory (~/mydir/ is used here as an example), and add the following environment variables:
Expand Down