Docker-in-Docker (DinD) capabilities of public runners deactivated. More info

Commit cce690b7 authored by DELMOTTE Stephane's avatar DELMOTTE Stephane
Browse files

ajout de la recette pour construire l'appliance

parent 8e99dbc7
- name: installation d'une instance cloud pour la formation ngs-2019
hosts: all
become: yes
become_method: sudo
tasks:
- name: installation des librairies et packages ubuntu...
apt:
name: "{{ item }}"
state: present
loop:
- libxml2-dev
- libncurses5-dev
- libtinfo-dev
- zlib1g-dev
- libbz2-dev
- liblzma-dev
- libcurl4-openssl-dev
- samtools
- bedtools
- hisat2
- igv
- python-matplotlib
- python-htseq
- libboost-iostreams1.65.1
- libssl-dev
- build-essential
- python2.7-dev
# - python-numphy
- python-matplotlib
- python-pysam
- python-htseq
- firefox
- unzip
- name: ajout de la signature pour R-3.6
apt_key:
keyserver: "hkp://keyserver.ubuntu.com:80"
id: E298A3A825C0D65DFD57CBB651716619E084DAB9
- name: ajout du dépot R-3.6
apt_repository:
repo: deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/
- name: installation de R-3.6
apt:
name: "{{ item }}"
state: present
loop:
- r-base
- r-base-dev
# - name: installation de quelques packages R
# command: /usr/bin/Rscript --slave --no-save --no-restore-history -e "install.packages(pkgs='{{ item }}', repos=c('https://pbil.univ-lyon1.fr/CRAN/'))"
# with_items:
# - BiocManager
# - name: installation de modules bioconductor
# command: /usr/bin/Rscript --slave --no-save --no-restore-history -e "BiocManager::install(c('{{ item }}'))"
# with_items:
# - DESeq2
# - name: telechargement de conda
# command: "wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh"
# - name: installation de conda
# command: "bash Miniconda3-latest-Linux-x86_64.sh -u -b -p /opt"
# - name: activation de l'environnement conda pour l'utilisateur root
# shell: "/opt/bin/conda init bash"
# - name: activation des chanels conda pour root
# shell: "/opt/bin/conda config --add channels {{ item }}"
# become: yes
# become_user: ubuntu
# with_items:
# - defaults
# - conda-forge
# - bioconda
# - name: installation des programmes via conda pour l'ensemble des utilisateurs
# command: "/opt/bin/conda install {{ item }} -y --channel bioconda"
# with_items:
# - fastqc
# - sra-tools
# - abyss
# - idba
# - name: creation de l'environnement myenv
# shell: "/opt/bin/conda create -y --name myenv"
# # become: yes
# # become_user: ubuntu
# - name: installation des package dans myenv pour l'utilisateur ubuntu
# shell: "/opt/bin/conda install {{ item }} -y --channel bioconda --name myenv"
# # become: yes
# # become_user: ubuntu
# with_items:
# # - ray
# - kmergenie
# - busco
# - quast
# - name: activation de l'environnement conda pour l'utilisateur root
# shell: "/opt/bin/conda init bash"
# become: yes
# become_user: ubuntu
# - name: copie du UrQt
# copy:
# src: ./UrQt
# dest: /usr/bin/
# mode: u+rwx,g-wx,o-rwx
# - name: rendre executable UrQt
# shell: "chmod +x /usr/bin/UrQt"
# - name: activation de l'environnement conda pour l'utilisateur root
# shell: "/opt/bin/conda init bash"
# become: yes
# become_user: ubuntu
# - name: Create du lien symbolique pour augustus
# file:
# src=/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.65.1
# dest=/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.60.0
# state=link
# - name: installation de pysam
# shell: "/opt/bin/pip install pysam"
# - name: création du groupe ngs
# group:
# name: ngs
# state: present
# - name: creation du repertoire /data
# file:
# path: /data
# state: directory
# group: ngs
# mode: '0755'
# - name: recupération de sspace_basic
# git:
# repo: 'https://github.com/nsoranzo/sspace_basic.git'
# dest: /data/sspace_basic
# update: no
# - name: copie de la configuration de busco
# copy:
# src: ./config.ini
# dest: /opt/envs/myenv/config
# mode: u+rwx,g+wx,o+rwx
# # création des utilisateurs et autorisation de login
# - name: enable login for stagiaire
# lineinfile:
# dest: /etc/ssh/sshd_config
# regexp: "^PasswordAuthentication no"
# line: "PasswordAuthentication yes"
# state: present
# - name: redemarre le service ssh
# service:
# name: ssh
# state: restarted
# - name: ajout des utilisateurs pour la formation
# user:
# name: stage1
# comment: stagiare1
# group: ngs
# append: yes
# shell: /bin/bash
# password: "$6$/AyVFCfXSm4tGJ$ephRS0A0t6xnGJ7i7PIXxOG2Y0R5FkFd9snIVRCKv4A5rbGZbUZw5/3C/zwYxHDGo90./YJgJEGCfYIema5Lq."
# - name: ajout des utilisateurs pour la formation
# user:
# name: stage2
# comment: stagiare2
# group: ngs
# append: yes
# shell: /bin/bash
# password: "$6$/AyVFCfXSm4tGJ$ephRS0A0t6xnGJ7i7PIXxOG2Y0R5FkFd9snIVRCKv4A5rbGZbUZw5/3C/zwYxHDGo90./YJgJEGCfYIema5Lq."
# - name: ajout des utilisateurs pour la formation
# user:
# name: stage3
# comment: stagiare3
# group: ngs
# append: yes
# shell: /bin/bash
# password: "$6$/AyVFCfXSm4tGJ$ephRS0A0t6xnGJ7i7PIXxOG2Y0R5FkFd9snIVRCKv4A5rbGZbUZw5/3C/zwYxHDGo90./YJgJEGCfYIema5Lq."
# - name: ajout des utilisateurs pour la formation
# user:
# name: stage4
# comment: stagiare4
# group: ngs
# append: yes
# shell: /bin/bash
# password: "$6$/AyVFCfXSm4tGJ$ephRS0A0t6xnGJ7i7PIXxOG2Y0R5FkFd9snIVRCKv4A5rbGZbUZw5/3C/zwYxHDGo90./YJgJEGCfYIema5Lq."
# - name: ajout des utilisateurs pour la formation
# user:
# name: stage5
# comment: stagiare5
# group: ngs
# append: yes
# shell: /bin/bash
# password: "$6$/AyVFCfXSm4tGJ$ephRS0A0t6xnGJ7i7PIXxOG2Y0R5FkFd9snIVRCKv4A5rbGZbUZw5/3C/zwYxHDGo90./YJgJEGCfYIema5Lq."
# - name: activation de l'environnement pour les nouveaux utilisateurs
# shell: 'su - {{ item }} -c "/opt/bin/conda init bash" '
# loop:
# - stage1
# - stage2
# - stage3
# - stage4
# - stage5
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