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add Xmipp and symbolic link

Merged Pullyvan Krishnamoorthy requested to merge new_scipion into master
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---
# tasks file for Scipion
- name: update ubuntu
become: yes
package:
update_cache: yes
upgrade: yes
##!!! depends on conda!!
- name: install Scipion requirements
become: yes
apt:
state: latest
pkg:
- openjdk-8-jdk
- libopenmpi-dev
- openmpi-bin
- gfortran
- libxft2
- libxss1
- gcc-5
- g++-5
- cmake
- openjdk-8-jdk
- libxft-dev
- libssl-dev
- libxext-dev
- libxml2-dev
- libreadline-dev
- libquadmath0
- libxslt1-dev
- gcc-8
- g++-8
- libopenmpi-dev
- openmpi-bin
- libxss-dev
- libgsl0-dev
- libx11-dev
- gfortran
- libfreetype6-dev
- scons
- libfftw3-dev
- libopencv-dev
- curl
- git
- unzip
- nmon
- name: check scipion scipion_conf/scipion.conf exist
become: yes
stat:
path: "{{ scipion_conf }}/scipion.conf"
register: scipion_conf_file
- name: Create scipion config directory
become: yes
file:
path: "{{ scipion_conf }}"
state: directory
mode: "0755"
#when: scipion_conf.stat.exists == True
- name: Scipion.conf
become: yes
template:
src: "templates/scipion.j2"
dest: "{{ scipion_conf }}/scipion.conf"
owner: root
group: root
mode: "0755"
backup: yes
when: scipion_conf_file.stat.exists == False
- name: hosts.conf
become: yes
template:
src: "templates/hosts.j2"
dest: "{{ scipion_conf }}/hosts.conf"
owner: root
group: root
mode: "0755"
backup: yes
- name: protocols.conf
become: yes
template:
src: "templates/protocols.j2"
dest: "{{ scipion_conf }}/protocols.conf"
owner: root
group: root
mode: "0755"
backup: yes
- name: create sciption folder in root directory
become: yes
file:
path: "{{ scipion_conf_root }}"
state: directory
mode: "0755"
- name: Create config file scipion for root
become: yes
template:
src: "templates/script_scipion_root.j2"
dest: "{{ scipion_conf_root }}/scipion.conf"
owner: root
group: root
mode: "0755"
backup: yes
- name: Create scipion config all users
become: yes
file:
path: "{{ scipion_conf }}"
state: directory
mode: "0755"
#when: scipion_conf.stat.exists == False
- name: Create config file scipion for all users
become: yes
template:
src: "templates/scipion.j2"
dest: "{{ scipion_conf }}/scipion.conf"
owner: root
group: root
mode: "0755"
backup: yes
- make
- python3-pip
- python3-mpi4py
- name: Check scipion Folder
become: yes
stat:
path: "{{ scipion_install_destination }}"
register: scipion_dir
- name: Create scipion directory
become: yes
file:
path: "{{ scipion_install_destination }}"
state: directory
mode: "0755"
- name: install scipion conda requirements
shell: source /usr/local/anaconda3/bin/activate && conda install -y -c anaconda mpi4py
args:
executable: /bin/bash
# when: scipion_dir.stat.exists == False
- name: "unzip the binaries of my software {{ scipion_install_version }} into {{ scipion_install_destination }}"
unarchive:
dest: "{{ scipion_install_destination }}"
src: "{{ scipion_repo_base_url }}/{{ scipion_versions[scipion_install_version]['url'] }}"
remote_src: yes
mode: "0755"
extra_opts:
- -P
- "{{ scipion_versions[scipion_install_version]['password'] }}"
- name: install scipion installer
# do not use offical pip
shell: source /usr/local/anaconda3/bin/activate && /usr/local/anaconda3/bin/pip install --user scipion-installer
args:
executable: /bin/bash
- name: Scipion installation
become: yes
command: ./scipion install
- name: install scipion
shell: source /usr/local/anaconda3/bin/activate && /usr/local/anaconda3/bin/python -m scipioninstaller -conda -noXmipp -noAsk /opt/scipion
args:
chdir: "{{ scipion_install_destination }}/scipion-master"
executable: /bin/bash
#when: scipion_dir.stat.exists == False
- name: check if scipion installed
become: yes
stat:
path: "{{ installed_path }}"
register: installed_scipion_post
- name: create config for scipion
shell: source /usr/local/anaconda3/bin/activate && /opt/scipion/scipion3 config --overwrite --unattended
args:
executable: /bin/bash
-name: install xmipp requirements
apt:
state: latest
pkg:
- scons
- libfftw3-dev
- libhdf5-dev
- python3-numpy
- python3-dev
- libtiff5-dev
- libsqlite3-dev
- default-jdk
- git
- cmake
- name: Install xmipp plugin
shell: /opt/scipion/scipion3 installp -p scipion-em-xmipp -j 12 | tee -a /tmp/xmipp_install.log
args:
executable: /bin/bash
- name: symbolic link for scipion
become: yes
file:
src: "{{ installed_path }}"
- name: Create a scipion symbolic link
ansible.builtin.file:
src: /opt/scipion/scipion3
dest: /usr/bin/scipion
state: link
- name: Scipion installp
become: yes
command: scipion installp -p {{ item }}
with_items:
- scipion-em-bionotes
- scipion-em-bsoft
- scipion-em-ccp4
- scipion-em-continuousflex
- scipion-em-cryoef
- scipion-em-cryomethods
- scipion-em-cryosparc2
- scipion-em-eman2
- scipion-em-empiar
- scipion-em-emxlib
- scipion-em-esrf
- scipion-em-grigoriefflab
- scipion-em-imagic
- scipion-em-localrec
- scipion-em-motioncorr
- scipion-em-phenix
- scipion-em-powerfit
- scipion-em-xmipp
# - scipion-em-relion Problem GCC version ask for before 6
- scipion-em-resmap
- scipion-em-simple
- scipion-em-sphire
- scipion-em-spider
- scipion-em-topaz
ignore_errors: yes
- name: Scipion xmipp bundle download
become: yes
git:
repo: "{{ dl_urs_git }}"
dest: "{{ scipion_xmipp }}/xmipp-bundle"
clone: yes
- name: Scipion xmipp installation
become: yes
command: ./xmipp get_devel_sources
args:
chdir: "{{ scipion_xmipp }}/xmipp-bundle"
ignore_errors: yes
- name: Scipion xmipp dev installation
shell: scipion installb xmippDev -j 8
- name: Create config file scipion for profile.d
become: yes
template:
src: "templates/scipion_profile_d.j2"
dest: "{{ scipion_profle_d }}/config_scipion.sh"
owner: root
group: root
mode: a+x
backup: yes
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