|
1 | | -BootStrap: docker |
2 | | -From: ubuntu:latest |
3 | | - |
4 | | -%labels |
5 | | - AUTHOR Nicolas Servant |
6 | | - |
7 | | -%pre |
8 | | - apt-get install -y debootstrap |
9 | | - |
10 | | -%files |
11 | | - environment.yml /opt/environment.yml |
12 | | - |
13 | | -%post |
14 | | - apt-get update |
15 | | - apt-get install -y wget |
16 | | - apt-get install -y gzip |
17 | | - apt-get install -y bzip2 |
18 | | - apt-get install -y curl |
19 | | - apt-get install -y unzip |
20 | | - |
21 | | - ## g++ |
22 | | - apt-get install -y build-essential |
23 | | - |
24 | | - # install anaconda |
25 | | - if [ ! -d /usr/local/anaconda ]; then |
26 | | - wget https://repo.continuum.io/miniconda/Miniconda3-4.5.4-Linux-x86_64.sh \ |
27 | | - -O ~/anaconda.sh && \ |
28 | | - bash ~/anaconda.sh -b -p /usr/local/anaconda && \ |
29 | | - rm ~/anaconda.sh |
30 | | - fi |
31 | | - |
32 | | - # set anaconda path |
33 | | - export PATH=$PATH:/usr/local/anaconda/bin |
34 | | - conda update conda |
35 | | - |
36 | | - conda config --add channels r |
37 | | - conda config --add channels defaults |
38 | | - conda config --add channels conda-forge |
39 | | - conda config --add channels bioconda |
40 | | - |
41 | | - # Let us save some space |
42 | | - conda clean --packages -y |
43 | | - |
44 | | - # external tools |
45 | | - echo "Installing conda environment ... " |
46 | | - conda env create -f /opt/environment.yml |
47 | | - echo "source activate HiC-Pro_v3.1.0" > ~/.bashrc |
48 | | - |
49 | | - # Install HiC-pro |
50 | | - echo "Installing latest HiC-Pro release ..." |
51 | | - VERSION=$(curl -s https://github.com/nservant/HiC-Pro/releases/latest | egrep -o 'v3.[0-9]*.[0-9]*') |
52 | | - echo "v"$VERSION".zip" | wget --base=http://github.com/nservant/HiC-Pro/archive/ -i - -O hicpro_latest.zip && unzip hicpro_latest.zip |
53 | | - #VERSION="devel_py3" |
54 | | - #echo $VERSION".zip" | wget --base=http://github.com/nservant/HiC-Pro/archive/ -i - -O hicpro_latest.zip && unzip hicpro_latest.zip |
55 | | - |
56 | | - cd $(echo HiC-Pro-$VERSION) |
57 | | - make configure |
58 | | - make install |
59 | | - |
60 | | - # Let us save some space |
61 | | - conda clean --packages -y |
62 | | - conda clean --all -y |
63 | | - rm -rf /usr/local/anaconda/pkgs |
64 | | - |
65 | | -%test |
66 | | - INSTALLED_HICPRO_VERSION=$(find /usr/local/bin -name HiC-Pro | xargs dirname) |
67 | | - $INSTALLED_HICPRO_VERSION/HiC-Pro -h |
68 | | - |
69 | | -%environment |
70 | | - export PATH=$PATH:/usr/local/anaconda/bin |
71 | | - INSTALLED_VERSION=$(find /usr/local/bin -name HiC-Pro | xargs dirname) |
72 | | - export PATH=$PATH:$INSTALLED_VERSION |
73 | | - export LANG=C |
| 1 | +BootStrap: docker |
| 2 | +From: ubuntu:latest |
| 3 | + |
| 4 | +%labels |
| 5 | + AUTHOR Nicolas Servant |
| 6 | + |
| 7 | +%files |
| 8 | + environment.yml /opt/environment.yml |
| 9 | + |
| 10 | +%environment |
| 11 | + export LANG=en_US.utf-8 |
| 12 | + export INSTALLED_VERSION=$(find /usr/local/bin -name HiC-Pro | xargs dirname) |
| 13 | + export PATH=$PATH:${INSTALLED_VERSION}:${INSTALLED_VERSION}/utils/ |
| 14 | + export PATH=/usr/local/conda/bin:$PATH |
| 15 | + source /opt/etc/bashrc |
| 16 | + |
| 17 | +%post |
| 18 | + apt-get update && \ |
| 19 | + apt-get install -y \ |
| 20 | + wget \ |
| 21 | + debootstrap \ |
| 22 | + gzip \ |
| 23 | + bzip2 \ |
| 24 | + curl \ |
| 25 | + unzip \ |
| 26 | + g++ \ |
| 27 | + |
| 28 | + # use bash as /bin/sh instead of dash (otherwise source /opt/etc/bashrc will not work) |
| 29 | + echo "dash dash/sh boolean false" | debconf-set-selections |
| 30 | + DEBIAN_FRONTEND=noninteractive dpkg-reconfigure dash |
| 31 | + |
| 32 | + # install miniconda |
| 33 | + if [ ! -d /usr/local/miniconda ]; then |
| 34 | + wget https://repo.continuum.io/miniconda/Miniconda3-py39_4.10.3-Linux-x86_64.sh -O miniconda.sh && \ |
| 35 | + sh miniconda.sh -b -p /usr/local/conda && \ |
| 36 | + rm miniconda.sh && \ |
| 37 | + ln -s /usr/local/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \ |
| 38 | + find /usr/local/conda/ -follow -type f -name '*.a' -delete && \ |
| 39 | + find /usr/local/conda/ -follow -type f -name '*.js.map' -delete && \ |
| 40 | + /usr/local/conda/bin/conda clean -afy |
| 41 | + fi |
| 42 | + |
| 43 | + # set miniconda path |
| 44 | + export PATH=/usr/local/conda/bin:$PATH |
| 45 | + conda update conda |
| 46 | + conda clean --packages -y |
| 47 | + |
| 48 | + #bashrc |
| 49 | + echo "#! /bin/bash\n\n" > ~/.bashrc |
| 50 | + conda init bash |
| 51 | + |
| 52 | + # external tools |
| 53 | + echo "Installing conda environment ... " |
| 54 | + conda env create -f /opt/environment.yml -n hicpro |
| 55 | + echo "conda activate hicpro" >> ~/.bashrc |
| 56 | + |
| 57 | + # Install HiC-pro |
| 58 | + export PATH=/usr/local/conda/envs/hicpro/bin:$PATH |
| 59 | + echo "Installing latest HiC-Pro release ..." |
| 60 | + #VERSION=$(curl -s https://github.com/nservant/HiC-Pro/releases/latest | egrep -o 'v3.[0-9]*.[0-9]*') |
| 61 | + VERSION="3.1.0" |
| 62 | + echo "v"$VERSION".zip" | wget --base=http://github.com/nservant/HiC-Pro/archive/ -i - -O hicpro_latest.zip && unzip hicpro_latest.zip |
| 63 | + |
| 64 | + cd $(echo HiC-Pro-$VERSION) |
| 65 | + make configure |
| 66 | + make install |
| 67 | + |
| 68 | + # Let us save some space |
| 69 | + conda clean --packages -y |
| 70 | + conda clean --all -y |
| 71 | + rm -rf /usr/local/miniconda/pkgs |
| 72 | + apt-get clean |
| 73 | + |
| 74 | + mkdir /opt/etc/ |
| 75 | + cp ~/.bashrc /opt/etc/bashrc |
| 76 | + |
| 77 | +%test |
| 78 | + INSTALLED_HICPRO_VERSION=$(find /usr/local/bin -name HiC-Pro | xargs dirname) |
| 79 | + ${INSTALLED_HICPRO_VERSION}/HiC-Pro -h |
| 80 | + |
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