From 0ef36e93bb364b78dc23153ab860dea52d821271 Mon Sep 17 00:00:00 2001 From: Christina K Date: Fri, 14 Apr 2023 17:49:55 -0500 Subject: [PATCH 1/2] Update README.md --- README.md | 29 ++++++++++++++++++++++++----- 1 file changed, 24 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 0b84549..1832c16 100644 --- a/README.md +++ b/README.md @@ -6,22 +6,41 @@ environment. Build instructions from [non-docker setting](https://github.com/kalininalab/alphafold_non_docker) by kalininalab were used. +## Setup + +Clone repository into your home directory and `cd` into the cloned folder. + ## Build container ``` # build base container -sudo /usr/software/singularity/bin/singularity build base.sif base.def +apptainer build base.sif base.def # build alphafold container -sudo /usr/software/singularity/bin/singularity build alphafold.sif alphafold.def +apptainer build alphafold.sif alphafold.def ``` -## Run AlphaFold +## Run AlphaFold Job + +Customize or add the following options to a typical CHTC HTCondor submit file: + ``` -./alphafold.py /path/to/fasta/file +universe = container +container_image = alphafold.sif +requirements = (HasGpulabData == true) + +transfer_executable = false +# replace with multimer.sh if applicable +executable = /opt/alphafold/monomer.sh +arguments = /gpulab_data/alphafold FASTA_file + +transfer_input_files = alphafold.sif, FASTA_file + +# request CPUs, GPUS, etc. ``` + ### Notes * The alphafold.py run script has no requirements and should run in vanilla python 3.8. * The run script allows customizing the database location and max_template_date. Call with `-h` to see usage information. * By default, this uses the `monomer` model for monomers and the `multimer` model for multimers, - and uses the `full_dbs` option for better quality results. For more details, see https://github.com/deepmind/alphafold#running-alphafold \ No newline at end of file + and uses the `full_dbs` option for better quality results. For more details, see https://github.com/deepmind/alphafold#running-alphafold From ebacf4350f2867fac19b97479c0db253e9fc43a4 Mon Sep 17 00:00:00 2001 From: Christina K Date: Fri, 14 Apr 2023 17:51:41 -0500 Subject: [PATCH 2/2] Update page to pull jax+CUDA Per https://github.com/google/jax/discussions/11443 --- alphafold.def | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/alphafold.def b/alphafold.def index f10d513..44bbf0a 100644 --- a/alphafold.def +++ b/alphafold.def @@ -28,7 +28,7 @@ From: base.sif wget -q -P alphafold/alphafold/common/ https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt pip install absl-py==0.13.0 biopython==1.79 chex==0.0.7 dm-haiku==0.0.4 dm-tree==0.1.6 immutabledict==2.0.0 jax==0.2.14 ml-collections==0.1.0 numpy==1.19.5 scipy==1.7.0 tensorflow==2.5.0 - pip install --upgrade jax jaxlib==0.1.69+cuda111 -f https://storage.googleapis.com/jax-releases/jax_releases.html + pip install --upgrade jax jaxlib==0.1.69+cuda111 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html pip install -r alphafold/requirements.txt cd /opt/miniconda3/envs/alphafold/lib/python3.8/site-packages/ && patch -p0 < $alphafold_path/docker/openmm.patch