Skip to content

GitLab

Switch branch/tag
Find file Normal viewHistoryPermalink
Dockerfile 1.54 KB
Newer Older
mashun1's avatar
dtk24.04.1  
mashun1 committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49 
FROM image.sourcefind.cn:5000/dcu/admin/base/jax:0.4.23-ubuntu20.04-dtk24.04.1-py3.10

# RUN apt update

# WORKDIR /app

# WORKDIR /app/softwares

# RUN git clone https://github.com/soedinglab/hh-suite.git

# RUN mkdir -p hh-suite/build && cd hh-suite/build && cmake -DCMAKE_INSTALL_PREFIX=. .. && make -j 4 && make install

# ENV PATH=/app/softwares/hh-suite/build/bin:/app/softwares/hh-suite/build/scripts:$PATH

# WORKDIR /app/softwares

# RUN wget https://github.com/TimoLassmann/kalign/archive/refs/tags/v3.4.0.zip && unzip v3.4.0.zip && cd kalign-3.4.0 && mkdir build && cd build && cmake .. && make && make install

# WORKDIR /app/softwares

# RUN sudo apt install doxygen -y

# RUN wget https://github.com/openmm/openmm/archive/refs/tags/8.0.0.zip && unzip 8.0.0.zip && cd openmm-8.0.0 && mkdir build && cd build && cmake .. && make && sudo make install && sudo make PythonInstall

# WORKDIR /app/softwares

# RUN wget https://github.com/openmm/pdbfixer/archive/refs/tags/1.9.zip && unzip 1.9.zip && cd pdbfixer-1.9 && python setup.py install 

# RUN sudo apt install hmmer -y

# WORKDIR /app

# COPY . /app/alphafold2

# RUN ls

# RUN pip install --no-cache-dir -r /app/alphafold2/requirements_dcu.txt -i https://mirrors.ustc.edu.cn/pypi/web/simple

# RUN pip install dm-haiku==0.0.11 flax==0.7.1 jmp==0.0.2 tabulate==0.8.9 --no-deps jax -i https://mirrors.ustc.edu.cn/pypi/web/simple

# RUN pip install orbax==0.1.6 orbax-checkpoint==0.1.6 optax==0.2.2 -i https://mirrors.ustc.edu.cn/pypi/web/simple

# WORKDIR /app/alphafold2

# RUN python setup.py install