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onlybelter/bio-info

By onlybelter

•Updated over 7 years ago

bioinformatics tools based on biostar-handbook and jupyter/scipy-notebook

Image
0

109

onlybelter/bio-info repository overview

⁠This image build on jupyter/datascience-notebook
  • all features in scipy-notebook⁠
  • jupyter/scipy-notebook version⁠:
    • Everything in jupyter/minimal-notebook and its ancestor images
    • pandas, numexpr, matplotlib, scipy, seaborn, scikit-learn, scikit-image, sympy, cython, patsy, statsmodel, cloudpickle, dill, numba, bokeh, sqlalchemy, hdf5,
    • vincent, beautifulsoup, protobuf, and xlrd packages
    • ipywidgets for interactive visualizations in Python notebooks
    • Facets for visualizing machine learning datasets
  • conda 4.6.8
  • Python v3.6.7
  • Java installed openjdk 11.0.1 2018-10-16 LTS
  • R v3.5.1 (bio-info:v2)
  • bioinformatics-related tools installed by conda (based on http://data.biostarhandbook.com/install/conda.txt⁠):
perl
perl-net-ssleay
seqkit
parallel
entrez-direct
minimap2
bwa
htslib
bowtie2
emboss
bedtools
samtools
bamtools
sra-tools
cutadapt
seqtk
datamash
bcftools
freebayes
subread
bioawk
hisat2
bbmap
trimmomatic
fastqc
snpeff
picard
blast
vt
readseq
deseq2 (bio-info:v2)
⁠Dockerfile:
# tag 41e066e5caa8 based on https://github.com/jupyter/docker-stacks/tree/41e066e5caa8b1a675b1b1730b4685db12671719
FROM jupyter/scipy-notebook:41e066e5caa8
MAINTAINER Xin Xiong <[email protected]>

ENV CONDA_MIRROR https://mirrors.tuna.tsinghua.edu.cn/anaconda

USER root

RUN apt-get update --fix-missing && \
    apt-get install -yq --no-install-recommends wget bzip2 ca-certificates \
    curl ncurses-dev byacc zlib1g-dev cmake python-pip \
    libhtml-parser-perl liblist-moreutils-perl libwww-perl \
    default-jdk ant ack-grep liblist-allutils-perl && \
    apt-get clean && \
    rm -rf /var/lib/apt/lists/*

USER $NB_UID

RUN conda update -y -n base conda

# add channels
RUN \
    conda config --add channels ${CONDA_MIRROR}/pkgs/free/ && \
    conda config --add channels ${CONDA_MIRROR}/pkgs/main/ && \
    conda config --add channels ${CONDA_MIRROR}/cloud/bioconda/ && \
    conda config --add channels ${CONDA_MIRROR}/cloud/conda-forge/ && \
    conda config --add channels ${CONDA_MIRROR}/cloud/pytorch/ && \
    conda config --set show_channel_urls yes && \
    fix-permissions $CONDA_DIR && \
    fix-permissions /home/$NB_USER

ADD ./install /tmp
# initialize the terminal based on the setting of biostarhandbook
RUN cat /tmp/bash_profile.txt >> ~/.bash_profile && \
    cat /tmp/bashrc.txt >> ~/.bashrc && \
    /bin/bash -c "source ~/.bash_profile"

# create a bio-info environment
RUN conda install --quiet --yes \
    perl perl-net-ssleay seqkit parallel entrez-direct minimap2 \
    bwa htslib bowtie2 emboss bedtools samtools bamtools sra-tools \
    cutadapt seqtk datamash bcftools freebayes subread bioawk \
    hisat2 bbmap trimmomatic fastqc snpeff picard blast vt readseq && \
    conda clean -tipsy && \
    fix-permissions $CONDA_DIR && \
    fix-permissions /home/$NB_USER

ENTRYPOINT [ "/usr/bin/tini", "--" ]
CMD [ "/bin/bash" ]
⁠Usage:

sudo docker push onlybelter/bio-info:v1 sudo docker run -it -v ~/:/mnt/data --entrypoint /bin/bash onlybelter/bio-info:v1

Tag summary

Content type

Image

Digest

Size

3 GB

Last updated

over 7 years ago

docker pull onlybelter/bio-info:v2