74 lines
2.4 KiB
Docker
74 lines
2.4 KiB
Docker
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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# SOFTWARE.
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ARG FROM_IMAGE_NAME=nvcr.io/nvidia/pytorch:21.09-py3
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FROM ${FROM_IMAGE_NAME} AS dgl_builder
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ENV DEBIAN_FRONTEND=noninteractive
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RUN apt-get update \
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&& apt-get install -y git build-essential python3-dev make cmake \
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&& rm -rf /var/lib/apt/lists/*
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WORKDIR /dgl
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RUN git clone --branch v0.7.0 --recurse-submodules --depth 1 https://github.com/dmlc/dgl.git .
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RUN sed -i 's/"35 50 60 70"/"60 70 80"/g' cmake/modules/CUDA.cmake
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WORKDIR build
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RUN cmake -DUSE_CUDA=ON -DUSE_FP16=ON ..
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RUN make -j8
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FROM ${FROM_IMAGE_NAME}
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# VERY IMPORTANT, DO NOT REMOVE:
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ENV FORCE_CUDA 1
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RUN pip install -v torch-geometric
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RUN pip install -v torch-scatter
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RUN pip install -v torch-sparse
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RUN pip install -v torch-cluster
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RUN pip install -v torch-spline-conv
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# copy built DGL and install it
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COPY --from=dgl_builder /dgl ./dgl
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RUN cd dgl/python && python setup.py install && cd ../.. && rm -rf dgl
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ENV DGLBACKEND=pytorch
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#RUN pip install dgl-cu111 -f https://data.dgl.ai/wheels/repo.html
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# HH-Suite
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RUN git clone https://github.com/soedinglab/hh-suite.git && \
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mkdir -p hh-suite/build
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WORKDIR hh-suite/build
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RUN cmake .. && \
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make && \
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make install
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# PSIPRED
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WORKDIR /workspace
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RUN wget http://wwwuser.gwdg.de/~compbiol/data/csblast/releases/csblast-2.2.3_linux64.tar.gz -O csblast-2.2.3.tar.gz && \
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mkdir -p csblast-2.2.3 && \
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tar xf csblast-2.2.3.tar.gz -C csblast-2.2.3 --strip-components=1 && \
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rm csblast-2.2.3.tar.gz
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RUN wget https://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/blast-2.2.26-x64-linux.tar.gz && \
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tar xf blast-2.2.26-x64-linux.tar.gz && \
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rm blast-2.2.26-x64-linux.tar.gz
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RUN wget http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/psipred.4.02.tar.gz && \
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tar xf psipred.4.02.tar.gz && \
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rm psipred.4.02.tar.gz
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ADD . /workspace/rf
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WORKDIR /workspace/rf
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RUN wget https://openstructure.org/static/lddt-linux.zip -O lddt.zip && unzip -d lddt -j lddt.zip
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RUN pip install --upgrade pip
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RUN pip install -r requirements.txt
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