diff --git a/Dockerfile b/Dockerfile index f06f4fa..ce9b970 100644 --- a/Dockerfile +++ b/Dockerfile @@ -34,40 +34,48 @@ 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 \ @@ -75,7 +83,8 @@ RUN pip install --upgrade pip && pip install \ 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 \ @@ -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 diff --git a/contrib/LKH-2.0.7.tgz b/contrib/LKH-2.0.7.tgz deleted file mode 100644 index 827a9ba..0000000 --- a/contrib/LKH-2.0.7.tgz +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:e224c7ac271b6ddbf5ff60c8c8b313d7078a99964fc0edf0c4791bb9fd449211 -size 815416 diff --git a/contrib/hdf5-1.8.18-linux-centos7-x86_64-gcc485-shared.tar.gz b/contrib/hdf5-1.8.18-linux-centos7-x86_64-gcc485-shared.tar.gz deleted file mode 100644 index 7066146..0000000 Binary files a/contrib/hdf5-1.8.18-linux-centos7-x86_64-gcc485-shared.tar.gz and /dev/null differ diff --git a/contrib/pkg_predictors.tar.gz b/contrib/pkg_predictors.tar.gz deleted file mode 100644 index f6c18ee..0000000 --- a/contrib/pkg_predictors.tar.gz +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:bf4298a4b7d8b0941f74d044b0f678735f4b4752623f81559136ae194939e2e3 -size 217241621