docker for run_blastplus_taxonserver WDL
987
has old 2.6.0 version of blast for Stephan's run_blastplus_taxserver.py
Blastn 2.6.0 seems to be incompatible with continuumio/miniconda2 image so I used a Dockerfile from Seung-jin and installed miniconda2.
FROM ubuntu:14.04
MAINTAINER Seung-Jin Sul <[email protected]>
RUN apt-get update && apt-get install -y \
curl \
cmake \
dh-autoreconf \
git \
libhdf5-serial-dev \
zlib1g-dev \
libncurses5-dev \
libncursesw5-dev \
make \
nano \
unzip \
vim \
wget \
--force-yes && \
apt-get autoclean && \
apt-get autoremove -y
RUN cd /opt && \
wget --no-check-certificate ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-x64-linux.tar.gz && \
tar -xvf ncbi-blast-2.6.0+-x64-linux.tar.gz && \
ln -s /opt/ncbi-blast-2.6.0+/bin/* /usr/local/bin/ && \
rm -rf ncbi-blast-2.6.0+-x64-linux.tar.gz
RUN wget https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh
RUN bash ./Miniconda2-latest-Linux-x86_64.sh -b
ENV PATH /root/miniconda2/bin:$PATH
RUN conda install -c anaconda requests==2.22.0
RUN conda install -c bioconda bbmap==38.68
COPY lib /blastplus/lib
COPY run_blastplus_taxserver.py /usr/local/bin
ENV PYTHONPATH /blastplus/lib
CMD ["bash"]
has blast version 2.9.0 which works in the debian OS which miniconda2 uses so I can run blastn for the blastplus wdl which uses sharding
FROM ubuntu:14.04
MAINTAINER jeff froula <[email protected]>
RUN apt-get update && apt-get install -y \
curl \
make \
wget \
vim
RUN wget https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh
RUN bash ./Miniconda2-latest-Linux-x86_64.sh -f -b -p /miniconda2
COPY lib /blastplus/lib
COPY bin/* /usr/local/bin/
ENV PATH /miniconda2/bin:$PATH
ENV PYTHONPATH /blastplus/lib
RUN conda install -c bioconda blast==2.9.0
RUN conda install -c anaconda requests==2.22.0
RUN conda install -c bioconda bbmap==38.68
Content type
Image
Digest
Size
637.5 MB
Last updated
over 6 years ago
docker pull jfroula/jaws-blastplus:1.1.1