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Jun 10, 2014 @chapmanb Update bcbio conda build to support latest bcbio-nextgen-vm. Clean up…
1 FROM stackbrew/ubuntu:14.04
Jan 7, 2014 @chapmanb Update bcbio-nextgen Dockerfile to provide clean build with minimal r…
2 MAINTAINER Brad Chapman "https://github.com/chapmanb"
3
4 # Setup a base system
Dec 14, 2015 @chapmanb v0.9.5 Dockerfile build
5 RUN apt-get update && \
Jul 28, 2016 @chapmanb Docker: minimize system dependencies in container
6 apt-get install -y curl wget git unzip tar gzip bzip2 xz-utils pigz && \
Jan 21, 2016 @chapmanb docker: system packages supporting Arvados
7 # Support inclusion in Arvados pipelines
8 apt-get install -y --no-install-recommends libcurl4-gnutls-dev mbuffer python2.7-dev python-virtualenv && \
Jul 28, 2016 @chapmanb Docker: minimize system dependencies in container
9 # Not added by default to save space
10 # apt-get install -y libglu1-mesa && \
Jan 7, 2014 @chapmanb Update bcbio-nextgen Dockerfile to provide clean build with minimal r…
11
12 # bcbio-nextgen installation
Nov 4, 2015 @chapmanb Create a single layer Dockerfile for hub.docker
13 mkdir -p /tmp/bcbio-nextgen-install && cd /tmp/bcbio-nextgen-install && \
Jan 7, 2014 @chapmanb Update bcbio-nextgen Dockerfile to provide clean build with minimal r…
14 wget --no-check-certificate \
15 https://raw.github.com/chapmanb/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py && \
Jul 4, 2014 @chapmanb Update dockerfile to be slightly more modular. Add documentation on s…
16 python bcbio_nextgen_install.py /usr/local/share/bcbio-nextgen \
May 9, 2016 @chapmanb Docker build: ensure tooldir specified
17 --isolate --nodata -u development --tooldir=/usr/local && \
Nov 4, 2015 @chapmanb Create a single layer Dockerfile for hub.docker
18 git config --global url.https://github.com/.insteadOf git://github.com/ && \
Jul 17, 2017 @chapmanb docker: remove mkl and mysql to reduce image size
19 /usr/local/share/bcbio-nextgen/anaconda/bin/conda install -y nomkl && \
Dec 14, 2015 @chapmanb v0.9.5 Dockerfile build
20 /usr/local/share/bcbio-nextgen/anaconda/bin/bcbio_nextgen.py upgrade --isolate --tooldir=/usr/local --tools && \
Feb 23, 2016 @chapmanb Add and document --datatarget option for data sets
21 /usr/local/share/bcbio-nextgen/anaconda/bin/bcbio_nextgen.py upgrade --isolate -u development --tools && \
Jul 17, 2017 @chapmanb docker: additional removal of large packages to reduce size
22 # Remove larger packages not used consistently in bcbio Docker runs
Jul 17, 2017 @chapmanb docker: remove mkl and mysql to reduce image size
23 /usr/local/share/bcbio-nextgen/anaconda/bin/conda remove --force -y mysql && \
Jul 18, 2017 @chapmanb docker: additional space cleanup to reduce image size
24 /usr/local/share/bcbio-nextgen/anaconda/bin/conda remove --force -y hap.py && \
25 /usr/local/share/bcbio-nextgen/anaconda/bin/conda remove --force -y bioconductor-org.hs.eg.db bioconductor-org.mm.eg.db bioconductor-go.db && \
Nov 4, 2015 @chapmanb Create a single layer Dockerfile for hub.docker
26
27 # setup paths
28 echo 'export PATH=/usr/local/bin:$PATH' >> /etc/profile.d/bcbio.sh && \
29
30 # add user run script
31 wget --no-check-certificate -O createsetuser \
32 https://raw.github.com/chapmanb/bcbio-nextgen-vm/master/scripts/createsetuser && \
33 chmod a+x createsetuser && mv createsetuser /sbin && \
34
35 # clean filesystem
Jan 21, 2016 @chapmanb Docker: cd out of removed directory
36 cd /usr/local && \
Jan 13, 2014 @chapmanb Unify align and align_pipe to avoid artificial distinction between pr…
37 apt-get clean && \
38 rm -rf /var/lib/apt/lists/* /var/tmp/* && \
39 /usr/local/share/bcbio-nextgen/anaconda/bin/conda clean --yes --tarballs && \
Jul 17, 2017 @chapmanb docker: additional removal of large packages to reduce size
40 # Remove large conda packages left behind
Jan 14, 2014 @chapmanb docker build: ensure environmental variables set even in non-interact…
41 rm -rf /usr/local/share/bcbio-nextgen/anaconda/pkgs/qt* && \
Jul 17, 2017 @chapmanb docker: additional removal of large packages to reduce size
42 rm -rf /usr/local/share/bcbio-nextgen/anaconda/pkgs/mysql-5.* && \
Jul 18, 2017 @chapmanb docker: additional space cleanup to reduce image size
43 rm -rf /usr/local/share/bcbio-nextgen/anaconda/pkgs/hap.py.* && \
Jul 18, 2017 @chapmanb Skip bwakit in hg38 without HLA typing enabled
44 rm -rf /usr/local/share/bcbio-nextgen/anaconda/pkgs/scipy-0.19.1-np113py27_nomkl_0 && \
Jul 17, 2017 @chapmanb docker: additional removal of large packages to reduce size
45 rm -rf /usr/local/share/bcbio-nextgen/anaconda/pkgs/bioconductor-org.*db* && \
Jul 18, 2017 @chapmanb docker: additional space cleanup to reduce image size
46 rm -rf /usr/local/share/bcbio-nextgen/anaconda/pkgs/bioconductor-go.*db* && \
Jul 17, 2017 @chapmanb docker: additional removal of large packages to reduce size
47 rm -rf /usr/local/share/bcbio-nextgen/anaconda/zulu*.tar.gz && \
Aug 1, 2015 @chapmanb Docker creation: fix download of pre-built genomes
48 rm -rf /usr/local/.git && \
Jan 7, 2014 @chapmanb Update bcbio-nextgen Dockerfile to provide clean build with minimal r…
49 rm -rf /.cpanm && \
Nov 4, 2015 @chapmanb Create a single layer Dockerfile for hub.docker
50 rm -rf /tmp/bcbio-nextgen-install && \
Jan 7, 2014 @chapmanb Update bcbio-nextgen Dockerfile to provide clean build with minimal r…
51
52 # Create directories and symlinks for data
Nov 4, 2015 @chapmanb Create a single layer Dockerfile for hub.docker
53 mkdir -p /mnt/biodata && \
Jan 7, 2014 @chapmanb Update bcbio-nextgen Dockerfile to provide clean build with minimal r…
54 mkdir -p /tmp/bcbio-nextgen && \
55 mv /usr/local/share/bcbio-nextgen/galaxy/bcbio_system.yaml /usr/local/share/bcbio-nextgen/config && \
56 rmdir /usr/local/share/bcbio-nextgen/galaxy && \
57 ln -s /mnt/biodata/galaxy /usr/local/share/bcbio-nextgen/galaxy && \
58 ln -s /mnt/biodata/gemini_data /usr/local/share/bcbio-nextgen/gemini_data && \
59 ln -s /mnt/biodata/genomes /usr/local/share/bcbio-nextgen/genomes && \
60 ln -s /mnt/biodata/liftOver /usr/local/share/bcbio-nextgen/liftOver && \
61 chmod a+rwx /usr/local/share/bcbio-nextgen && \
62 chmod a+rwx /usr/local/share/bcbio-nextgen/config && \
63 chmod a+rwx /usr/local/share/bcbio-nextgen/config/*.yaml && \
64
Jan 23, 2014 @chapmanb Update docker file to ensure leninent permissions on /usr/local direc…
65 # Ensure permissions are set for update in place by arbitrary users
Nov 4, 2015 @chapmanb Create a single layer Dockerfile for hub.docker
66 find /usr/local -perm /u+x -execdir chmod a+x {} \; && \
67 find /usr/local -perm /u+w -execdir chmod a+w {} \;