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Merge pull request #11 from FRED-2/internal/removed-contrib
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[INTERNAL]Changed Dockerfile to sourceforge contrib
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b-schubert authored Jan 25, 2017
2 parents b139aa8 + 441a6b1 commit b44f2e5
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63 changes: 31 additions & 32 deletions Dockerfile
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Expand Up @@ -34,48 +34,57 @@ RUN apt-get update && apt-get install -y software-properties-common \
libboost-dev \
&& update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 60 --slave /usr/bin/g++ g++ /usr/bin/g++-4.9 \
&& rm -rf /var/lib/apt/lists/* \
&& curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | bash \
&& apt-get install -y git-lfs \
&& git lfs install \
&& apt-get clean \
&& apt-get purge


RUN git clone https://github.com/FRED-2/ImmunoNodes.git \
&& cd /ImmunoNodes \
&& git lfs fetch \
&& ls -lah contrib\
&& git lfs pull \
&& chmod -R 777 /ImmunoNodes/ \
&& ls -lah contrib \
&& mkdir /usr/src/LKH \
&& tar -xzf /ImmunoNodes/contrib/pkg_predictors.tar.gz -C /usr/local/ \
&& tar -xzf /ImmunoNodes/contrib/LKH-2.0.7.tgz -C /usr/src/LKH \
&& make -C /usr/src/LKH/LKH-2.0.7 \
&& mv /usr/src/LKH/LKH-2.0.7/LKH /usr/local/bin/
&& make -C /ImmunoNodes/src \
&& chmod -R 777 /ImmunoNodes/

#get contribs
RUN mkdir /usr/src/LKH \
&& mkdir /usr/src/hdf5 \
&& curl -o /ImmunoNodes/src/data/tries/uniprot_proteome_l8.trie "https://netcologne.dl.sourceforge.net/project/immunonode-files/uniprot_proteome_l8.trie" \
&& curl -o /ImmunoNodes/src/data/tries/uniprot_proteome_l9.trie "https://netcologne.dl.sourceforge.net/project/immunonode-files/uniprot_proteome_l9.trie" \
&& curl -o /ImmunoNodes/src/data/tries/uniprot_proteome_l10.trie "https://netcologne.dl.sourceforge.net/project/immunonode-files/uniprot_proteome_l10.trie" \
&& curl -o /ImmunoNodes/src/data/tries/uniprot_proteome_l11.trie "https://netcologne.dl.sourceforge.net/project/immunonode-files/uniprot_proteome_l11.trie" \
&& curl -o /usr/local/pkg_predictors.tar.gz "https://netcologne.dl.sourceforge.net/project/immunonode-files/contrib/pkg_predictors.tar.gz" \
&& curl -o /usr/src/LKH/LKH-2.0.7.tgz "https://netcologne.dl.sourceforge.net/project/immunonode-files/contrib/LKH-2.0.7.tgz" \
&& curl -o /usr/src/hdf5/hdf5.tar.gz "https://netcologne.dl.sourceforge.net/project/immunonode-files/contrib/hdf5-1.8.18-linux-centos7-x86_64-gcc485-shared.tar.gz" \
&& tar -xzf /usr/local/pkg_predictors.tar.gz -C /usr/local/ \
&& tar -xzf /usr/src/LKH/LKH-2.0.7.tgz -C /usr/src/LKH/ \
&& tar -xvf /usr/src/hdf5/hdf5.tar.gz -C /usr/src/hdf5/ \
&& mv /usr/src/hdf5/hdf5-1.8.18-linux-centos7-x86_64-gcc485-shared/bin/* /usr/local/bin/ \
&& mv /usr/src/hdf5/hdf5-1.8.18-linux-centos7-x86_64-gcc485-shared/lib/* /usr/local/lib/ \
&& mv /usr/src/hdf5/hdf5-1.8.18-linux-centos7-x86_64-gcc485-shared/include/* /usr/local/include/ \
&& mv /usr/src/hdf5/hdf5-1.8.18-linux-centos7-x86_64-gcc485-shared/share/* /usr/local/share/ \
&& make -C /usr/src/LKH/LKH-2.0.7/ \
&& mv /usr/src/LKH/LKH-2.0.7/LKH /usr/local/bin/ \
&& rm -rf /usr/src/LKH/ \
&& rm -f /usr/local/pkg_predictors.tar.gz \
&& rm -rf /usr/src/hdf5/



#HLA Typing
#OptiType dependecies
RUN tar -xvf /ImmunoNodes/contrib/hdf5-1.8.18-linux-centos7-x86_64-gcc485-shared.tar.gz -C /ImmunoNodes/contrib/ \
&& mv /ImmunoNodes/contrib/hdf5-1.8.18-linux-centos7-x86_64-gcc485-shared/bin/* /usr/local/bin/ \
&& mv /ImmunoNodes/contrib/hdf5-1.8.18-linux-centos7-x86_64-gcc485-shared/lib/* /usr/local/lib/ \
&& mv /ImmunoNodes/contrib/hdf5-1.8.18-linux-centos7-x86_64-gcc485-shared/include/* /usr/local/include/ \
&& mv /ImmunoNodes/contrib/hdf5-1.8.18-linux-centos7-x86_64-gcc485-shared/share/* /usr/local/share/ \
&& rm -rf /ImmunoNodes/contrib/


ENV LD_LIBRARY_PATH /usr/local/lib:$LD_LIBRARY_PATH
ENV HDF5_DIR /usr/local/

RUN pip install --upgrade pip && pip install \
setuptools==33.1.1 \
cython \
numpy \
pyomo \
pysam \
matplotlib \
tables \
pandas \
future
future \
&& pip install git+https://github.com/FRED-2/Fred2@master

#installing optitype form git repository (version Dec 09 2015) and wirtig config.ini
RUN git clone https://github.com/FRED-2/OptiType.git \
Expand Down Expand Up @@ -112,18 +121,8 @@ RUN hg clone https://bitbucket.org/sebastian_boegel/seq2hla \
&& chmod 777 /usr/local/bin/seq2hla/seq2HLA.py

#Fred2
RUN pip install git+https://github.com/FRED-2/Fred2@master


#dist2self
#download pre-generated tries
RUN curl -o /ImmunoNodes/src/data/tries/uniprot_proteome_l8.trie "https://netcologne.dl.sourceforge.net/project/immunonode-files/uniprot_proteome_l8.trie" \
&& curl -o /ImmunoNodes/src/data/tries/uniprot_proteome_l9.trie "https://netcologne.dl.sourceforge.net/project/immunonode-files/uniprot_proteome_l9.trie" \
&& curl -o /ImmunoNodes/src/data/tries/uniprot_proteome_l10.trie "https://netcologne.dl.sourceforge.net/project/immunonode-files/uniprot_proteome_l10.trie" \
&& curl -o /ImmunoNodes/src/data/tries/uniprot_proteome_l11.trie "https://netcologne.dl.sourceforge.net/project/immunonode-files/uniprot_proteome_l11.trie"
#RUN pip install --upgrade pip && pip install git+https://github.com/FRED-2/Fred2@master

#compile code
RUN make -C /ImmunoNodes/src

#set envirnomental variables for prediction methods
ENV NETCHOP /usr/local/predictors/netchop/netchop-3.1
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3 changes: 0 additions & 3 deletions contrib/LKH-2.0.7.tgz
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3 changes: 0 additions & 3 deletions contrib/pkg_predictors.tar.gz
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