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Update alphafold images and Dockerfiles #136

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merged 5 commits into from
Mar 22, 2024
Merged

Update alphafold images and Dockerfiles #136

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c57f9cf
Update alphafold standard container
JoseEspinosa Mar 18, 2024
f5d4bf1
Update dockerfile alphafold standard
JoseEspinosa Mar 19, 2024
def38fd
Update docker image for af2 msa for testing
JoseEspinosa Mar 19, 2024
400ce19
Update alphafold dockerfiles
JoseEspinosa Mar 20, 2024
d54e571
Use dev image for split mode (prediction step)
JoseEspinosa Mar 20, 2024
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12 changes: 5 additions & 7 deletions dockerfiles/Dockerfile_nfcore-proteinfold_alphafold2_msa
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Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
FROM nvidia/cuda:11.4.2-cudnn8-runtime-ubuntu18.04
LABEL authors="Luisa Santus, Athanasios Baltzis, Leila Mansouri" \
FROM nvidia/cuda:11.4.3-cudnn8-runtime-ubuntu18.04

LABEL authors="Luisa Santus, Athanasios Baltzis, Jose Espinosa-Carrasco, Leila Mansouri" \
title="nfcore/proteinfold_alphafold2_msa" \
Version="1.1.0" \
description="Docker image containing all software requirements to run the RUN_ALPHAFOLD2_MSA module using the nf-core/proteinfold pipeline"


# Use bash to support string substitution.
SHELL ["/bin/bash", "-o", "pipefail", "-c"]

Expand All @@ -29,7 +29,7 @@ RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install --no-instal
# Clone AlphaFold2
RUN git clone https://github.com/cbcrg/alphafold.git /app/alphafold && \
cd /app/alphafold && \
git checkout b35b26e0ef88cc00498a73a8dffe429a119c6ee4 && \
git checkout 1b3170e9409472ec8ad044f9935c92bedd7b4674 && \
cd -

# Compile HHsuite from source
Expand All @@ -48,13 +48,11 @@ RUN wget -q -P /tmp \
&& rm /tmp/Miniconda3-latest-Linux-x86_64.sh

# Install conda packages
RUN /conda/bin/conda install -qy conda=4.13.0 \
&& /conda/bin/conda install -y -c conda-forge \
RUN /conda/bin/conda install -y -c conda-forge \
pip \
python=3.10 \
&& conda clean --all --force-pkgs-dirs --yes

# Install pip packages
RUN pip3 install --upgrade pip --no-cache-dir \
&& pip3 install -r /app/alphafold/requirements_msa.txt --no-cache-dir

13 changes: 5 additions & 8 deletions dockerfiles/Dockerfile_nfcore-proteinfold_alphafold2_split
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Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
FROM nvidia/cuda:11.4.2-cudnn8-runtime-ubuntu18.04
LABEL authors="Athanasios Baltzis, Leila Mansouri" \
FROM nvidia/cuda:11.4.3-cudnn8-runtime-ubuntu18.04

LABEL authors="Athanasios Baltzis, Jose Espinosa-Carrasco, Leila Mansouri" \
title="nfcore/proteinfold_alphafold2_split" \
Version="1.1.0" \
description="Docker image containing all software requirements to run the RUN_ALPHAFOLD2_PRED module using the nf-core/proteinfold pipeline"


# Use bash to support string substitution.
SHELL ["/bin/bash", "-o", "pipefail", "-c"]

Expand All @@ -29,7 +29,7 @@ RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install --no-instal
# Clone AlphaFold2
RUN git clone https://github.com/cbcrg/alphafold.git /app/alphafold && \
cd /app/alphafold && \
git checkout b35b26e0ef88cc00498a73a8dffe429a119c6ee4 && \
git checkout 1b3170e9409472ec8ad044f9935c92bedd7b4674 && \
cd -

# Compile HHsuite from source
Expand All @@ -48,8 +48,7 @@ RUN wget -q -P /tmp \
&& rm /tmp/Miniconda3-latest-Linux-x86_64.sh

# Install conda packages
RUN /conda/bin/conda install -qy conda=4.13.0 \
&& /conda/bin/conda install -y -c conda-forge \
RUN /conda/bin/conda install -y -c conda-forge \
openmm=7.7.0 \
cudatoolkit==11.1.1 \
pdbfixer \
Expand All @@ -60,7 +59,6 @@ RUN /conda/bin/conda install -qy conda=4.13.0 \
RUN wget -q -P /app/alphafold/alphafold/common/ \
https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt


# Install pip packages.
RUN pip3 install --upgrade pip --no-cache-dir \
&& pip3 install -r /app/alphafold/requirements.txt --no-cache-dir \
Expand All @@ -79,4 +77,3 @@ RUN chmod u+s /sbin/ldconfig.real
# details.
RUN cd /app/alphafold
RUN ldconfig

13 changes: 5 additions & 8 deletions dockerfiles/Dockerfile_nfcore-proteinfold_alphafold2_standard
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Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
FROM nvidia/cuda:11.4.2-cudnn8-runtime-ubuntu18.04
LABEL authors="Athanasios Baltzis, Leila Mansouri" \
FROM nvidia/cuda:11.4.3-cudnn8-runtime-ubuntu18.04

LABEL authors="Athanasios Baltzis, Jose Espinosa-Carrasco, Leila Mansouri" \
title="nfcore/proteinfold_alphafold2_standard" \
Version="1.1.0" \
description="Docker image containing all software requirements to run the RUN_ALPHAFOLD2 module using the nf-core/proteinfold pipeline"


# Use bash to support string substitution.
SHELL ["/bin/bash", "-o", "pipefail", "-c"]

Expand All @@ -29,7 +29,7 @@ RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install --no-instal
# Clone AlphaFold2
RUN git clone https://github.com/deepmind/alphafold.git /app/alphafold && \
cd /app/alphafold && \
git checkout 6a3af1adb3bbbc53562da100e3819b2fc882f915 && \
git checkout 7c9114c8423ac9db981d8365168464bab09b3e54 && \
cd -

# Compile HHsuite from source
Expand All @@ -48,16 +48,14 @@ RUN wget -q -P /tmp \
&& rm /tmp/Miniconda3-latest-Linux-x86_64.sh

# Install conda packages
RUN /conda/bin/conda install -qy conda=4.13.0 \
&& /conda/bin/conda install -y -c conda-forge \
RUN /conda/bin/conda install -y -c conda-forge \
openmm=7.7.0 \
cudatoolkit==11.1.1 \
pdbfixer \
pip \
python=3.10 \
&& conda clean --all --force-pkgs-dirs --yes

COPY . /app/alphafold
RUN wget -q -P /app/alphafold/alphafold/common/ \
https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt

Expand All @@ -79,4 +77,3 @@ RUN chmod u+s /sbin/ldconfig.real
# details.
RUN cd /app/alphafold
RUN ldconfig

2 changes: 1 addition & 1 deletion modules/local/run_alphafold2.nf
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Expand Up @@ -5,7 +5,7 @@ process RUN_ALPHAFOLD2 {
tag "$meta.id"
label 'process_medium'

container "nf-core/proteinfold_alphafold2_standard:1.1.0"
container "nf-core/proteinfold_alphafold2_standard:dev"

input:
tuple val(meta), path(fasta)
Expand Down
2 changes: 1 addition & 1 deletion modules/local/run_alphafold2_msa.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ process RUN_ALPHAFOLD2_MSA {
tag "$meta.id"
label 'process_medium'

container "nf-core/proteinfold_alphafold2_msa:1.1.0"
container "nf-core/proteinfold_alphafold2_msa:dev"

input:
tuple val(meta), path(fasta)
Expand Down
2 changes: 1 addition & 1 deletion modules/local/run_alphafold2_pred.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ process RUN_ALPHAFOLD2_PRED {
tag "$meta.id"
label 'process_medium'

container "nf-core/proteinfold_alphafold2_split:1.1.0"
container "nf-core/proteinfold_alphafold2_split:dev"

input:
tuple val(meta), path(fasta)
Expand Down
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