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Commit fd834042 authored by Cedric Cabau's avatar Cedric Cabau
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Fix Dockerfile for busco version 3.0

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tags/drap-v1.91/doc/lib/src/Dockerfile
+ 19
− 16
View file @ fd834042
......@@ -88,22 +88,6 @@ RUN cd /usr/local/bin \
&& wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat \
&& chmod +x blat
## -- install busco -- ##
RUN cd /usr/local/src \
&& git clone --recursive https://gitlab.com/ezlab/busco.git \
&& cd busco \
&& curl -SL http://busco.ezlab.org/v2/datasets/vertebrata_odb9.tar.gz | tar -xz \
&& curl -SL http://busco.ezlab.org/v2/datasets/metazoa_odb9.tar.gz | tar -xz \
&& curl -SL http://busco.ezlab.org/v2/datasets/eukaryota_odb9.tar.gz | tar -xz \
&& curl -SL http://busco.ezlab.org/v2/datasets/arthropoda_odb9.tar.gz | tar -xz \
&& curl -SL http://busco.ezlab.org/v2/datasets/fungi_odb9.tar.gz | tar -xz \
&& curl -SL http://busco.ezlab.org/v2/datasets/bacteria_odb9.tar.gz | tar -xz \
&& python setup.py install \
&& cat config/config.ini.default | sed -e 's|/home/osboxes.*|/usr/bin/|' > config/config.ini \
&& chmod +x scripts/run_BUSCO.py scripts/generate_plot.py \
&& ln -s $PWD/scripts/run_BUSCO.py /usr/local/bin/run_BUSCO.py \
&& ln -s $PWD/scripts/generate_plot.py /usr/local/bin/generate_plot.py
## -- install fastq_illumina_filter -- ##
RUN cd /usr/local/bin \
&& wget http://cancan.cshl.edu/labmembers/gordon/fastq_illumina_filter/release/0.1/fastq_illumina_filter-Linux-x86_64 \
......@@ -151,6 +135,25 @@ RUN cd /usr/local/src \
&& rm -f bin/librt.so.1
ENV PATH /usr/local/src/transrate-1.0.3-linux-x86_64:/usr/local/src/transrate-1.0.3-linux-x86_64/bin:/usr/local/src/transrate-1.0.3-linux-x86_64/lib/app/ruby/2.2.0/bin:$PATH
## -- install busco -- ##
RUN cd /usr/local/src \
&& git clone --recursive https://gitlab.com/ezlab/busco.git \
&& cd busco \
&& curl -SL http://busco.ezlab.org/v2/datasets/vertebrata_odb9.tar.gz | tar -xz \
&& curl -SL http://busco.ezlab.org/v2/datasets/metazoa_odb9.tar.gz | tar -xz \
&& curl -SL http://busco.ezlab.org/v2/datasets/eukaryota_odb9.tar.gz | tar -xz \
&& curl -SL http://busco.ezlab.org/v2/datasets/arthropoda_odb9.tar.gz | tar -xz \
&& curl -SL http://busco.ezlab.org/v2/datasets/fungi_odb9.tar.gz | tar -xz \
&& curl -SL http://busco.ezlab.org/v2/datasets/bacteria_odb9.tar.gz | tar -xz \
&& python setup.py install
RUN cd /usr/local/src/busco \
&& mv config/config.ini.default config/config.ini \
&& sed -i -e 's|/home/osboxes.*|/usr/bin/|' config/config.ini \
&& chmod +x scripts/run_BUSCO.py scripts/generate_plot.py \
&& ln -s $PWD/scripts/run_BUSCO.py /usr/local/bin/run_BUSCO.py \
&& ln -s $PWD/scripts/generate_plot.py /usr/local/bin/generate_plot.py
## -- loading the adapter and contamination databases for TSA compliance -- ##
RUN mkdir /usr/local/src/banks \
&& cd /usr/local/src/banks \
......
trunk/doc/lib/src/Dockerfile
+ 19
− 16
View file @ fd834042
......@@ -88,22 +88,6 @@ RUN cd /usr/local/bin \
&& wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat \
&& chmod +x blat
## -- install busco -- ##
RUN cd /usr/local/src \
&& git clone --recursive https://gitlab.com/ezlab/busco.git \
&& cd busco \
&& curl -SL http://busco.ezlab.org/v2/datasets/vertebrata_odb9.tar.gz | tar -xz \
&& curl -SL http://busco.ezlab.org/v2/datasets/metazoa_odb9.tar.gz | tar -xz \
&& curl -SL http://busco.ezlab.org/v2/datasets/eukaryota_odb9.tar.gz | tar -xz \
&& curl -SL http://busco.ezlab.org/v2/datasets/arthropoda_odb9.tar.gz | tar -xz \
&& curl -SL http://busco.ezlab.org/v2/datasets/fungi_odb9.tar.gz | tar -xz \
&& curl -SL http://busco.ezlab.org/v2/datasets/bacteria_odb9.tar.gz | tar -xz \
&& python setup.py install \
&& cat config/config.ini.default | sed -e 's|/home/osboxes.*|/usr/bin/|' > config/config.ini \
&& chmod +x scripts/run_BUSCO.py scripts/generate_plot.py \
&& ln -s $PWD/scripts/run_BUSCO.py /usr/local/bin/run_BUSCO.py \
&& ln -s $PWD/scripts/generate_plot.py /usr/local/bin/generate_plot.py
## -- install fastq_illumina_filter -- ##
RUN cd /usr/local/bin \
&& wget http://cancan.cshl.edu/labmembers/gordon/fastq_illumina_filter/release/0.1/fastq_illumina_filter-Linux-x86_64 \
......@@ -151,6 +135,25 @@ RUN cd /usr/local/src \
&& rm -f bin/librt.so.1
ENV PATH /usr/local/src/transrate-1.0.3-linux-x86_64:/usr/local/src/transrate-1.0.3-linux-x86_64/bin:/usr/local/src/transrate-1.0.3-linux-x86_64/lib/app/ruby/2.2.0/bin:$PATH
## -- install busco -- ##
RUN cd /usr/local/src \
&& git clone --recursive https://gitlab.com/ezlab/busco.git \
&& cd busco \
&& curl -SL http://busco.ezlab.org/v2/datasets/vertebrata_odb9.tar.gz | tar -xz \
&& curl -SL http://busco.ezlab.org/v2/datasets/metazoa_odb9.tar.gz | tar -xz \
&& curl -SL http://busco.ezlab.org/v2/datasets/eukaryota_odb9.tar.gz | tar -xz \
&& curl -SL http://busco.ezlab.org/v2/datasets/arthropoda_odb9.tar.gz | tar -xz \
&& curl -SL http://busco.ezlab.org/v2/datasets/fungi_odb9.tar.gz | tar -xz \
&& curl -SL http://busco.ezlab.org/v2/datasets/bacteria_odb9.tar.gz | tar -xz \
&& python setup.py install
RUN cd /usr/local/src/busco \
&& mv config/config.ini.default config/config.ini \
&& sed -i -e 's|/home/osboxes.*|/usr/bin/|' config/config.ini \
&& chmod +x scripts/run_BUSCO.py scripts/generate_plot.py \
&& ln -s $PWD/scripts/run_BUSCO.py /usr/local/bin/run_BUSCO.py \
&& ln -s $PWD/scripts/generate_plot.py /usr/local/bin/generate_plot.py
## -- loading the adapter and contamination databases for TSA compliance -- ##
RUN mkdir /usr/local/src/banks \
&& cd /usr/local/src/banks \
......
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