├── logo └── logo_python_final.png ├── biopython-tutorial └── Dockerfile ├── biopython-buildbot └── Dockerfile ├── biopython-notebook ├── Dockerfile └── startup.sh ├── biopython-sql └── Dockerfile ├── README.rst ├── biopython └── Dockerfile ├── LICENSE.BSD-3-Clause └── LICENSE.Biopython /logo/logo_python_final.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biopython/biopython_docker/HEAD/logo/logo_python_final.png -------------------------------------------------------------------------------- /biopython-tutorial/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biopython/biopython-notebook 2 | MAINTAINER Tiago Antao 3 | 4 | ENV JUPYTER_HOME /scratch/biopython-notebook/notebooks 5 | 6 | RUN git clone https://github.com/tiagoantao/biopython-notebook.git 7 | 8 | WORKDIR /scratch/biopython-notebook/notebooks 9 | -------------------------------------------------------------------------------- /biopython-buildbot/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biopython/biopython-sql:latest 2 | MAINTAINER Tiago Antao 3 | 4 | ENV DEBIAN_FRONTEND noninteractive 5 | 6 | #BuildBot 7 | RUN apt-get update 8 | RUN apt-get install -y buildbot-slave git 9 | 10 | RUN buildslave create-slave biopython testing.open-bio.org:9989 CHANGEUSER CHANGEPASS 11 | 12 | RUN echo "buildslave start biopython" >> entrypoint.sh 13 | RUN echo "tail -f biopython/twistd.log" >> entrypoint.sh 14 | 15 | ENTRYPOINT bash entrypoint.sh 16 | -------------------------------------------------------------------------------- /biopython-notebook/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biopython/biopython-sql:latest 2 | MAINTAINER Tiago Antao 3 | 4 | ENV DEBIAN_FRONTEND noninteractive 5 | 6 | WORKDIR / 7 | #IPython notebook 8 | RUN apt-get install --force-yes -y python3-zmq python3-jinja2 9 | RUN pip3 install pyzmq --upgrade 10 | RUN pip3 install jupyter --upgrade 11 | RUN mkdir scratch 12 | WORKDIR scratch 13 | ADD startup.sh /usr/bin/startup 14 | RUN chmod +x /usr/bin/startup 15 | ENV JUPYTER_USER=jupyteruser \ 16 | JUPYTER_UID=1555 \ 17 | JUPYTER_GID=1555 \ 18 | JUPYTER_HOME=/scratch 19 | #CMD jupyter notebook --no-browser --ip=* --port=9803 20 | EXPOSE 9803 9803 21 | CMD /usr/bin/startup 22 | -------------------------------------------------------------------------------- /biopython-notebook/startup.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | BLUE='\033[0;34m' 4 | GREEN='\033[0;32m' 5 | NC='\033[0m' 6 | 7 | if ! id -u $JUPYTER_USER > /dev/null 2>&1; then 8 | echo -e "use local user: " ${BLUE}$JUPYTER_USER${NC} 9 | addgroup --gid $JUPYTER_UID $JUPYTER_USER 10 | adduser --uid $JUPYTER_UID --gid $JUPYTER_UID --gecos "" --shell /bin/bash --disabled-password --home $JUPYTER_HOME --no-create-home $JUPYTER_USER 11 | fi 12 | 13 | if [ -e $JUPYTER_HOME ]; 14 | then 15 | echo -e ${GREEN}$JUPYTER_HOME${NC} exists 16 | chown -R $JUPYTER_UID $JUPYTER_HOME 17 | chgrp -R $JUPYTER_UID $JUPYTER_HOME 18 | else 19 | mkdir -p $JUPYTER_HOME 20 | chown -R $JUPYTER_UID $JUPYTER_HOME 21 | fi 22 | 23 | 24 | su $JUPYTER_USER -c "jupyter notebook --no-browser --ip=* --port=9803" 25 | -------------------------------------------------------------------------------- /biopython-sql/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biopython/biopython:latest 2 | MAINTAINER Tiago Antao 3 | 4 | ENV DEBIAN_FRONTEND noninteractive 5 | 6 | #For BioSQL 7 | RUN apt-get install -y --force-yes postgresql python3-psycopg2 8 | RUN apt-get install -y --force-yes mysql-server python-mysqldb 9 | RUN apt-get install -y --force-yes python3-mysql.connector 10 | RUN apt-get install -y --force-yes postgresql-server-dev-9.5 11 | RUN apt-get clean 12 | 13 | RUN pip3 install psycopg2 --upgrade 14 | 15 | #Database servers 16 | RUN echo "host all all ::1/128 trust" > /etc/postgresql/9.5/main/pg_hba.conf 17 | RUN echo "service postgresql start" > .bashrc 18 | RUN echo "service mysql start" >> .bashrc 19 | RUN echo "export LANG=en_GB.UTF-8" >> .bashrc 20 | RUN echo "service postgresql start" > entrypoint.sh 21 | RUN echo "service mysql start" >> entrypoint.sh 22 | -------------------------------------------------------------------------------- /README.rst: -------------------------------------------------------------------------------- 1 | Docker containers for Biopython 2 | =============================== 3 | 4 | .. image:: logo/logo_python_final.png 5 | :scale: 40 % 6 | :align: center 7 | 8 | Here you can find Docker containers that include Biopython. 9 | 10 | To install these you will need Docker (https://www.docker.com/) 11 | on Linux or Docker Toolbox (https://www.docker.com/products/docker-toolbox) on Windows/Mac. 12 | 13 | All containers should include all dependencies which can be installed 14 | without licensing/copyright issues. 15 | 16 | There are 5 containers available at this time: 17 | 18 | * A basic one where you ssh into to use it. No databases included. 19 | 20 | * A basic one where you ssh into to use it. With BioSQL. 21 | 22 | * One with a Jupyter (IPython Notebook) interface, 23 | 24 | * One with a Jupyter (IPython Notebook) interface including a Biopython 25 | tutorial. 26 | 27 | * One for buildbot integration testing. 28 | 29 | 30 | For each container there will be 2 versions: for Python 3 and legacy Python 2. 31 | For now only Python 3 is available. 32 | 33 | Installation and Usage 34 | ====================== 35 | 36 | Basic container 37 | --------------- 38 | 39 | In the basic container, you ssh into it and use it from there. 40 | 41 | Python 3:: 42 | 43 | docker pull biopython/biopython 44 | docker run -t -i biopython/biopython /bin/bash 45 | python3 # inside the container 46 | 47 | BioSQL container 48 | ---------------- 49 | 50 | Python 3:: 51 | 52 | docker pull biopython/biopython-sql 53 | docker run -t -i biopython/biopython-sql /bin/bash 54 | python3 # inside the container 55 | 56 | Jupyter container 57 | ----------------- 58 | 59 | Here you will need to point your browser to localhost:9803 (or 9802 on Python 60 | 2). 61 | 62 | **If you are on boot2docker you need to do an extra port mapping step on your 63 | VM** 64 | 65 | Python 3:: 66 | 67 | docker pull biopython/biopython-notebook 68 | docker run -p 9803:9803 -t -i biopython/biopython-notebook 69 | 70 | Jupyter container with tutorials 71 | -------------------------------- 72 | 73 | Here you will need to point your browser to localhost:9803 (or 9802 on Python 74 | 2). 75 | 76 | **If you are on boot2docker you need to do an extra port mapping step on your 77 | VM** 78 | 79 | Python 3:: 80 | 81 | docker pull biopython/biopython-tutorial 82 | docker run -p 9803:9803 -t -i biopython/biopython-tutorial 83 | 84 | Mount your local directory to Docker (here are are naming it $PWD/scratch, but 85 | change it as preferred):: 86 | 87 | docker run -v $PWD:/scratch -e JUPYTER_UID=$UID -it -p 9803:9803 biopython-notebook 88 | 89 | Buildbot version 90 | ================ 91 | 92 | **You only need this if you help with our testing effort** 93 | 94 | You will need to manually download the Docker file and update 95 | 96 | CHANGEUSER CHANGEPASS 97 | 98 | to your buildbot username and password 99 | 100 | Python 3:: 101 | 102 | #do this in an empty directory 103 | wget https://raw.githubusercontent.com/biopython/biopython_docker/master/biopython-buildbot/Dockerfile 104 | #REMEMBER TO CHANGE CHANGEUSER AND CHANGEPASS 105 | docker build -t biopython-buildbot . 106 | docker run -t -i biopython-buildbot 107 | 108 | 109 | LICENSING 110 | ========= 111 | 112 | The software herein is made available under a dual license under the 113 | Biopython historic license (see file LICENSE.Biopython) and the 3-clause 114 | BSD license (see file LICENSE.BSD-3-Clause) 115 | 116 | Logo credits and copyright: Vincent Davis 117 | 118 | Authors: Tiago Antao and Tao Zhang with help from Björn Grüning 119 | -------------------------------------------------------------------------------- /biopython/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM ubuntu:16.04 2 | MAINTAINER Tiago Antao 3 | 4 | ENV DEBIAN_FRONTEND noninteractive 5 | #We need this for phylip 6 | RUN echo 'deb http://archive.ubuntu.com/ubuntu xenial multiverse' >> /etc/apt/sources.list \ 7 | && apt-get update \ 8 | && apt-get upgrade -y --force-yes \ 9 | && apt-get install -y --force-yes \ 10 | build-essential \ 11 | git \ 12 | python3-numpy \ 13 | wget \ 14 | gcc \ 15 | g++ \ 16 | python3-dev \ 17 | unzip \ 18 | make \ 19 | python3-matplotlib \ 20 | python3-reportlab \ 21 | python3-pip r-base \ 22 | clustalw \ 23 | fasttree \ 24 | t-coffee python3-pil \ 25 | bwa \ 26 | ncbi-blast+ \ 27 | emboss \ 28 | clustalo \ 29 | phylip \ 30 | mafft \ 31 | muscle \ 32 | samtools \ 33 | phyml \ 34 | wise \ 35 | raxml \ 36 | language-pack-en \ 37 | paml \ 38 | probcons \ 39 | python3-pandas \ 40 | python3.5-dev \ 41 | libxft-dev \ 42 | && apt-get clean 43 | 44 | #for Phylo_CDAO 45 | # RUN pip3 install pip --upgrade 46 | RUN pip3 install rdflib --upgrade \ 47 | && pip3 install cython --upgrade \ 48 | && pip3 install numpy --upgrade \ 49 | && pip3 install Pillow --upgrade \ 50 | && pip3 install matplotlib --upgrade \ 51 | && pip3 install pandas --upgrade 52 | 53 | #Manual software 54 | RUN echo "export DIALIGN2_DIR=/tmp" >> .bashrc 55 | 56 | #reportlab fonts 57 | RUN wget http://www.reportlab.com/ftp/fonts/pfbfer.zip 58 | WORKDIR cd /usr/lib/python3.4/dist-packages/reportlab 59 | RUN mkdir fonts 60 | WORKDIR cd /usr/lib/python3.4/dist-packages/reportlab/fonts 61 | RUN unzip /pfbfer.zip \ 62 | && mkdir -p /usr/lib/python3.5/dist-packages/reportlab/fonts 63 | WORKDIR /usr/lib/python3.5/dist-packages/reportlab/fonts 64 | RUN unzip /pfbfer.zip 65 | WORKDIR / 66 | RUN rm pfbfer.zip 67 | 68 | #genepop 69 | RUN mkdir genepop 70 | WORKDIR /genepop 71 | RUN wget http://kimura.univ-montp2.fr/~rousset/sources.tar.gz \ 72 | && tar zxf sources.tar.gz \ 73 | && g++ -DNO_MODULES -o Genepop GenepopS.cpp -O3 \ 74 | && cp Genepop /usr/bin 75 | WORKDIR / 76 | RUN rm -rf genepop 77 | 78 | #fdist 79 | RUN mkdir fdist2 80 | WORKDIR /fdist2 81 | RUN wget http://www.maths.bris.ac.uk/~mamab/software/fdist2.zip \ 82 | && unzip fdist2.zip \ 83 | && gcc -o fdist2 -O fdist2.c -lm \ 84 | && gcc -o cplot -O cplot.c as100.c as99.c -lm \ 85 | && gcc -o pv -O pv.c as100.c as99.c -lm \ 86 | && gcc -o datacal -O datacal.c -lm \ 87 | && cp datacal pv cplot fdist2 /usr/bin 88 | WORKDIR / 89 | RUN rm -rf fdist2 90 | 91 | 92 | #dfdist 93 | RUN wget http://www.maths.bris.ac.uk/~mamab/stuff/Dfdist_a.zip \ 94 | && unzip Dfdist_a 95 | WORKDIR Dfdist_a 96 | RUN gcc -O -o Ddatacal Ddatacal.c -lm \ 97 | && gcc -O -o Dfdist Dfdist.c -lm \ 98 | && gcc -O -o pv2 pv2.c -lm \ 99 | && gcc -O -o cplot2 cplot2.c -lm \ 100 | && cp pv2 Dfdist Ddatacal cplot2 /usr/bin 101 | WORKDIR / 102 | RUN rm -rf Dfdist_a* 103 | 104 | #msaprobs 105 | RUN wget "http://sourceforge.net/projects/msaprobs/files/latest/download?source=files" -O MSA.tar.gz \ 106 | && tar zxf MSA.tar.gz 107 | WORKDIR /MSAProbs-0.9.7/MSAProbs 108 | RUN make \ 109 | && cp msaprobs /usr/bin 110 | WORKDIR / 111 | 112 | #fastsimcoal 113 | RUN wget http://cmpg.unibe.ch/software/fastsimcoal2/downloads/fsc_linux64.zip \ 114 | && unzip fsc_linux64.zip \ 115 | && chmod a+x fsc_linux64/fsc25221 \ 116 | && cp fsc_linux64/fsc25221 /usr/bin/fsc252 \ 117 | && rm -rf fsc_* 118 | 119 | #DSSP 120 | RUN wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64 \ 121 | && mv dssp-2.0.4-linux-amd64 /usr/bin/dssp \ 122 | && chmod a+x /usr/bin/dssp 123 | 124 | #XXmotif 125 | WORKDIR /usr/local/bin 126 | RUN wget "http://xxmotif.genzentrum.lmu.de/index.php?id=download&version=64" -O xx.tar.gz \ 127 | && tar zxf xx.tar.gz \ 128 | && rm xx.tar.gz 129 | WORKDIR / 130 | ENV PYTHON_PATH /biopython 131 | 132 | #Biopython 133 | RUN git clone https://github.com/biopython/biopython.git 134 | WORKDIR /biopython 135 | RUN python3.5 setup.py install 136 | 137 | #set default python version to 3.5 138 | RUN touch ~/.bash_aliases \ 139 | && echo alias python=\'python3.5\' > ~/.bash_aliases 140 | -------------------------------------------------------------------------------- /LICENSE.BSD-3-Clause: -------------------------------------------------------------------------------- 1 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | The BSD 3-Clause License | Open Source Initiative 12 | 13 | 14 | 15 | 16 | 17 | 20 | 21 | 26 | 27 | 28 | 31 | 32 |
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Note: You may omit clause 3 and still be OSD-conformant. Despite its colloquial name "BSD New", this is not the newest version of the BSD license; it was followed by the even newer BSD-2-Clause version, sometimes known as the "Simplified BSD License". On January 9th, 2008 the OSI Board approved BSD-2-Clause, which is used by FreeBSD and others. It omits the final "no-endorsement" clause and is thus roughly equivalent to the MIT License.

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Biopython License Agreement
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