ajout de la recette pour construire l'appliance

appliance.yml

+- 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