From ebd82cf4a642a7a1583b24cb0f830ad60535f21b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bertrand=20N=C3=A9ron?= <bneron@pasteur.fr>
Date: Thu, 2 Dec 2021 15:11:52 +0100
Subject: [PATCH] update playbook for 2021 course
migrate to ubuntu
update list of software
---
.gitlab-ci.yml | 2 +-
Docker/Dockerfile | 8 +-
Inventory/group_vars/all | 44 +++-----
Inventory/hosts | 2 +-
README.md | 52 ++++-----
phylogeny.yml | 4 +-
roles/gensoft/tasks/main.yml | 18 ++--
.../files/usr/share/applications/lsd.desktop | 10 --
roles/lsd/tasks/main.yml | 18 ----
roles/pastml/tasks/main.yml | 4 +-
roles/system/tasks/main.yml | 102 ++++++++++--------
roles/tcoffee/tasks/main.yml | 63 -----------
12 files changed, 106 insertions(+), 221 deletions(-)
delete mode 100644 roles/lsd/files/usr/share/applications/lsd.desktop
delete mode 100644 roles/lsd/tasks/main.yml
delete mode 100644 roles/tcoffee/tasks/main.yml
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 37adae5..3139e79 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -5,7 +5,7 @@ stages:
testing:
stage: test
- image: registry-gitlab.pasteur.fr/hub-courses/phylogeny-machines/phylogeny-ci
+ image: registry-gitlab.pasteur.fr/hub-courses/phylogeny-machines/phylogeny_ci
script:
- chmod 755 $CI_PROJECT_DIR
- ansible-playbook --limit gitlab phylogeny.yml
diff --git a/Docker/Dockerfile b/Docker/Dockerfile
index 91cc703..0e1fb5e 100644
--- a/Docker/Dockerfile
+++ b/Docker/Dockerfile
@@ -1,10 +1,8 @@
-FROM centos:centos7
+FROM ubuntu:focal
MAINTAINER Bertrand Neron <bneron@pasteur.fr>
USER root
-RUN yum clean all &&\
- yum update -y &&\
- yum install -y epel-release &&\
- yum install -y ansible
\ No newline at end of file
+RUN apt-get update -y &&\
+ apt-get install -y ansible
diff --git a/Inventory/group_vars/all b/Inventory/group_vars/all
index c559642..225c88a 100644
--- a/Inventory/group_vars/all
+++ b/Inventory/group_vars/all
@@ -1,41 +1,29 @@
---
gensoft_packs:
- - {name: beast, vers: 'v2.4.7'}
+ - {name: beast, vers: 'v2.6.2'}
+ - {nane: beagle, vers: '5.1'}
- {name: BMGE, vers: '1.12'}
- {name: Clustal-Omega, vers: '1.2.4'}
- {name: ClustalW, vers: '2.1'}
- {name: fastme, vers: '2.1.6.1'}
- - {name: FigTree, vers: '1.4.3'}
+ - {name: FigTree, vers: '1.4.4'}
+ - {name: goalign, vers: '0.3.5'}
+ - {name: gotree, vers: '0.4.2'}
- {name: gblocks, vers: '0.91b'}
- - {name: IQ-TREE, vers: '1.6.3'}
+ - {name: iq-tree, vers: '2.0.6'}
- {name: jmodeltest2, vers: '2.1.10'}
- - {name: mafft, vers: '7.407'} #7.407
- - {name: mrbayes, vers: '3.2.6'}
+ - {name: lsd2, vers: '1.9.7'}
+ - {name: mafft, vers: '7.467'} #7.407
+ - {name: mrbayes, vers: '3.2.7'}
- {name: msaprobs, vers: '1.0.5'}
- {name: muscle, vers: '3.8.31'}
- - {name: paml, vers: '4.9e'}
+ - {name: paml, vers: '4.9j'}
- {name: pamlX, vers: '1.3.1'}
- {name: phylip, vers: '3.67'}
- - {name: phyml, vers: '3.1'}
- - {name: seaview, vers: '4.6.2.1'}
-
-gensoft_menu:
- - {pack_name: seaview, bin_name: seaview, vers: '4.6.2.1', term: 'false'}
- - {pack_name: FigTree, bin_name: figtree, vers: '1.4.3', term: 'false'}
- - {pack_name: pamlX, bin_name: pamlX, vers: '1.3.1', term: 'false'}
- - {pack_name: beast, bin_name: beast, vers: 'v2.1.2', term: 'true'}
- - {pack_name: ClustalW, bin_name: clustalw, vers: '2.1', term: 'true'}
- - {pack_name: fastme, bin_name: fastme, vers: '2.1.4', term: 'true'}
- - {pack_name: gblocks, bin_name: Gblocks, vers: '0.91b', term: 'true'}
- - {pack_name: mafft, bin_name: mafft, vers: '7.310', term: 'true'}
- - {pack_name: mrbayes, bin_name: mb, vers: '3.2.6', term: 'true'}
- - {pack_name: phylip, bin_name: protpars, vers: '3.67', term: 'true'}
- - {pack_name: phylip, bin_name: dnapars, vers: '3.67', term: 'true'}
- - {pack_name: phylip, bin_name: protdist, vers: '3.67', term: 'true'}
- - {pack_name: phylip, bin_name: dnadist, vers: '3.67', term: 'true'}
- - {pack_name: phylip, bin_name: neighbor, vers: '3.67', term: 'true'}
- - {pack_name: phylip, bin_name: consense, vers: '3.67', term: 'true'}
- - {pack_name: phylip, bin_name: drawtree, vers: '3.67', term: 'true'}
- - {pack_name: phylip, bin_name: drawgram, vers: '3.67', term: 'true'}
- - {pack_name: phylip, bin_name: seqboot, vers: '3.67', term: 'true'}
+ - {name: phyml, vers: '3.3.20190909'}
+ - {name: raxml, vers: '8.2.12'}
+ - {name: raxml-ng, vers: '1.0'}
+ - {name: seaview, vers: '5.0.1'}
+ - {name: tracer, vers: '1.7.1'}
+ - {name: treetime, vers: '0.7.4'}
diff --git a/Inventory/hosts b/Inventory/hosts
index d8a244f..320fc59 100644
--- a/Inventory/hosts
+++ b/Inventory/hosts
@@ -8,6 +8,6 @@
157.99.191.[172:175]
-[phylogeny-ci]
+[phylogeny_ci]
gitlab ansible_connection=local
diff --git a/README.md b/README.md
index b14ea68..10d948d 100644
--- a/README.md
+++ b/README.md
@@ -6,22 +6,27 @@ It also use *gensoft* yum repository then it will work for hosts operating *Cent
The installed packages are:
- beast
+- beagle
- bmge
-- clustalW
- clustaO
+- clustalW
- fastme
- FigTree
- IQ-TREE
+- goalign
+- gotree
- jmodeltest2
+- lsd
- mafft
-- mr bayes
+- mrbayes
- msaprobs
- muscle
-- palm and pamlx
+- palm
+- raxml
+- raxml-ng
- seaview
-- tcoffee
+- tracer
- pastml
-- lsd
and
- the libreoffice suite
@@ -44,29 +49,8 @@ and
The framework used to install the host is ansible.
So if you are not familiar with it, please check the [ansible documentation](http://docs.ansible.com/ansible/latest/index.html).
-Ansible need to be installed on the local host,
-python >= 2.6, <3 and ssh must be installed on the remote hosts
-
-## copy your public key to the remote host
-
-First you have to copy your public shh key on each remote hosts using ssh-copy-id
-for instance on host 157.99.191.140:
-
-```
-ssh-copy-id -i ~/.ssh/id_rsa.pub 157.99.191.140
-/usr/bin/ssh-copy-id: INFO: Source of key(s) to be installed: "/home/bneron/.ssh/id_rsa.pub"
-/usr/bin/ssh-copy-id: INFO: attempting to log in with the new key(s), to filter out any that are already installed
-/usr/bin/ssh-copy-id: INFO: 1 key(s) remain to be installed -- if you are prompted now it is to install the new keys
-bneron@157.99.191.140's password:
-
-Number of key(s) added: 1
-
-Now try logging into the machine, with: "ssh '157.99.191.140'"
-and check to make sure that only the key(s) you wanted were added.
-```
-
-*note: if you want to add key in root account `ssh-copy-id -i ~/.ssh/id_rsa.pub root@157.99.191.140`
-which is the default for this ansible playbook.*
+Ansible needs to be installed on the local host,
+python >= 2.7 or >=3.5 and ssh must be installed on the remote hosts
## play the ansible playbook
@@ -81,17 +65,17 @@ vim Inventory/hosts
then run it
```
-ansible-playbook phylogeny.yml
+ansible-playbook --limit phylogeny -u formateur --ask-pass --become phylogeny.yml
```
-If you want to play only one or a set of playbook see available tags in phylogeny.yml
+If you want to play only one or a set of playbook see available tags in practices.yml then add option `-t <tag>`
then run
```
-ansible-playbook -t editors phylogeny.yml
+ansible-playbook --limit phylogeny -u formateur --ask-pass --become -t editors phylogeny.yml
```
-# how to installed a new soft
+# how to install a new soft
# from a gensoft package
@@ -106,7 +90,7 @@ just add an item in the gensoft_packs dict located Inventory/group_vars/all file
You have to write a new role and add it in the phylogeny.yml playbook
and play the role
-# add an entry in the phylogenie menu
+# add an entry in the phylogeny menu
If the entry you want to add is installed via gensoft (see above),
you just have to add an item in the gensoft_menu dict located Inventory/group_vars/all files
@@ -124,7 +108,7 @@ then play the tag menu
ansible-playbook -t menu phylogeny.yml
```
-if i'ts a new gensoft package run the entire role gensoft:
+if it's a new gensoft package run the entire role gensoft:
```
ansible-playbook -t gensoft phylogeny.yml
diff --git a/phylogeny.yml b/phylogeny.yml
index 1a221c1..cb5b2f9 100644
--- a/phylogeny.yml
+++ b/phylogeny.yml
@@ -1,6 +1,6 @@
---
- name: Install software required by the Phylogeny course
- hosts: phylogeny:phylogeny-ci
+ hosts: phylogeny:phylogeny_ci
remote_user: root
roles:
@@ -8,7 +8,5 @@
- {role: editors, tags: ['editors']}
- {role: office, tags: ['office']}
- {role: gensoft, tags: ['gensoft']}
- - {role: tcoffee, tags: ['tcoffee']}
- {role: pastml, tags: ['pastml']}
- - {role: lsd, tags: ['lsd']}
diff --git a/roles/gensoft/tasks/main.yml b/roles/gensoft/tasks/main.yml
index b49f4a1..63fda89 100644
--- a/roles/gensoft/tasks/main.yml
+++ b/roles/gensoft/tasks/main.yml
@@ -1,10 +1,10 @@
---
- name: Intstalling gensoft scientific pacakges
- yum:
+ ansible.builtin.apt:
name: "gensoft-{{ item.name }}-{{ item.vers }}"
state: latest
- with_items: "{{ gensoft_packs }}"
+ loop: "{{ gensoft_packs|flatten(levels=1) }}"
- name: Load all modules by default system wide
@@ -14,10 +14,10 @@
mode: 0644
-- name: Put application in Menu
- template:
- src: templates/usr/share/applications/template.desktop.j2
- dest: "/usr/share/applications/{{ item.bin_name }}.desktop"
- with_items: "{{ gensoft_menu }}"
- tags: menu
-
+# - name: Put application in Menu
+# template:
+# src: templates/usr/share/applications/template.desktop.j2
+# dest: "/usr/share/applications/{{ item.bin_name }}.desktop"
+# with_items: "{{ gensoft_menu }}"
+# tags: menu
+#
diff --git a/roles/lsd/files/usr/share/applications/lsd.desktop b/roles/lsd/files/usr/share/applications/lsd.desktop
deleted file mode 100644
index 795de2a..0000000
--- a/roles/lsd/files/usr/share/applications/lsd.desktop
+++ /dev/null
@@ -1,10 +0,0 @@
-# {{ ansible_managed }}
-[Desktop Entry]
-Version=v0.3.2-beta
-Name=lsd
-Exec=/usr/local/bin/lsd
-Type=Application
-Terminal=true
-Categories=Phylogeny;
-StartupWMClass=lsd
-X-Desktop-File-Install-Version=0.15
\ No newline at end of file
diff --git a/roles/lsd/tasks/main.yml b/roles/lsd/tasks/main.yml
deleted file mode 100644
index 883be34..0000000
--- a/roles/lsd/tasks/main.yml
+++ /dev/null
@@ -1,18 +0,0 @@
----
-
-- name: Set lsd prefix
- set_fact:
- lsd_prefix: /usr/local
- lsd_version: v0.3.3
-
-- name: Downloading lsd binary
- get_url:
- url: "https://github.com/tothuhien/lsd-0.3beta/releases/download/{{ lsd_version }}/lsd_unix"
- dest: "{{ lsd_prefix }}/bin/lsd"
- mode: 555
-
-- name: Put lsd in Menu
- copy:
- src: files/usr/share/applications/lsd.desktop
- dest: /usr/share/applications/lsd.desktop
- mode: 0644
diff --git a/roles/pastml/tasks/main.yml b/roles/pastml/tasks/main.yml
index e75cf5f..dfbbdaa 100644
--- a/roles/pastml/tasks/main.yml
+++ b/roles/pastml/tasks/main.yml
@@ -2,10 +2,10 @@
- name: Install Python3
yum:
- name: ['python36', 'python36-pip']
+ name: ['python3', 'python3-pip']
state: latest
- name: Install PastML
pip:
- executable: pip3.6
+ executable: pip3
name: pastml
diff --git a/roles/system/tasks/main.yml b/roles/system/tasks/main.yml
index bcc4d8e..55e8e6d 100644
--- a/roles/system/tasks/main.yml
+++ b/roles/system/tasks/main.yml
@@ -1,28 +1,35 @@
---
-- name: Install EPEL repo.
- yum:
- name: https://dl.fedoraproject.org/pub/epel/epel-release-latest-{{ ansible_distribution_major_version }}.noarch.rpm
- state: present
+- name: Installing gnupg2
+ ansible.builtin.apt:
+ name: gnupg2
+ state: latest
+
-- name: Import EPEL GPG key.
- rpm_key:
- key: /etc/pki/rpm-gpg/RPM-GPG-KEY-EPEL-{{ ansible_distribution_major_version }}
+- name: Download the gensoft debian packages signing key
+ ansible.builtin.apt_key:
+ url: http://mirrors.web.pasteur.fr/gensoft/ubuntu/deb/public.pgp
state: present
+
- name: add gensoft repos
- yum_repository:
- name: gensoft
- description: packages provided by pasteur
- baseurl: http://mirrors.web.pasteur.fr/gensoft/rpm/
- gpgcheck: no
+ ansible.builtin.apt_repository:
+ filename: gensoft.list
+ repo: "deb http://mirrors.web.pasteur.fr/gensoft/ubuntu/deb/ /"
+ update_cache: yes
+ state: present
+
+- name: add gensoft private repos
+ ansible.builtin.apt_repository:
+ filename: gensoft_private.list
+ repo: "deb http://mirrors.web.pasteur.fr/gensoft/ubuntu/deb_private/ /"
+ update_cache: yes
+ state: present
-- name: upgrade all packages
- yum: name=* state=latest update_cache=yes
- name: install general dependencies
- yum:
- name: ['zlib-devel', 'readline-devel', 'make', 'unzip', 'tar', 'gensoft-modules-3.3', 'gensoft-gcc-4.9.0' ]
+ ansible.builtin.apt:
+ pkg: ['zlib1g-dev', 'libreadline-dev', 'make', 'unzip', 'tar', 'gensoft-modules-4.4.0', 'gensoft-gcc-10.1.0' ]
state: latest
- name: Create gensoft group
@@ -39,35 +46,36 @@
shell: /bin/bash
state: present
-- name: Check whether Phylogeny exist in applications menu"
- command: grep -Fq "<Directory>Phylogeny.directory</Directory>" /etc/xdg/menus/applications.menu
- register: check_menu
- check_mode: no
- ignore_errors: yes
- changed_when: no
-
-- name: Create an entry in applications menu
- when: check_menu.rc == 1
- blockinfile:
- marker: ''
- path: /etc/xdg/menus/applications.menu
- insertafter: "^.*<!-- End Internet -->.*$"
- content: |
- <!-- Phylogeny -->
- <Menu>
- <Name>Phylogeny</Name>
- <Directory>Phylogeny.directory</Directory>
- <Include>
- <And>
- <Category>Phylogeny</Category>
- <Not><Category>Settings</Category></Not>
- </And>
- </Include>
- </Menu>
- <!-- End Phylogeny -->
-- name: Create Phylogeny menu
- copy:
- src: files/usr/share/desktop-directories/Phylogeny.directory
- dest: /usr/share/desktop-directories/Phylogeny.directory
- mode: 0644
+# - name: Check whether Phylogeny exist in applications menu"
+# command: grep -Fq "<Directory>Phylogeny.directory</Directory>" /etc/xdg/menus/applications.menu
+# register: check_menu
+# check_mode: no
+# ignore_errors: yes
+# changed_when: no
+#
+# - name: Create an entry in applications menu
+# when: check_menu.rc == 1
+# blockinfile:
+# marker: ''
+# path: /etc/xdg/menus/applications.menu
+# insertafter: "^.*<!-- End Internet -->.*$"
+# content: |
+# <!-- Phylogeny -->
+# <Menu>
+# <Name>Phylogeny</Name>
+# <Directory>Phylogeny.directory</Directory>
+# <Include>
+# <And>
+# <Category>Phylogeny</Category>
+# <Not><Category>Settings</Category></Not>
+# </And>
+# </Include>
+# </Menu>
+# <!-- End Phylogeny -->
+#
+# - name: Create Phylogeny menu
+# copy:
+# src: files/usr/share/desktop-directories/Phylogeny.directory
+# dest: /usr/share/desktop-directories/Phylogeny.directory
+# mode: 0644
diff --git a/roles/tcoffee/tasks/main.yml b/roles/tcoffee/tasks/main.yml
deleted file mode 100644
index 50af2ba..0000000
--- a/roles/tcoffee/tasks/main.yml
+++ /dev/null
@@ -1,63 +0,0 @@
----
-
-- name: Set tcoffee prefix
- set_fact:
- tcoffee_prefix: /usr/local
- tcoffee_version: T-COFFEE_installer_Version_12.00.7fb08c2_linux_x64
-
-- name: Creating dir source for t-coffee
- file:
- path: "{{ tcoffee_prefix }}/src/tcoffee"
- state: directory
-
-
-- name: Downloading t-coffee
- get_url:
- url: " http://www.tcoffee.org/Packages/Stable/Latest/{{ tcoffee_version }}.tar.gz"
- dest: "{{ tcoffee_prefix }}/src/tcoffee"
-
-
-- name: Unarchive t-coffee
- unarchive:
- src: "{{ tcoffee_prefix }}/src/tcoffee/{{ tcoffee_version }}.tar.gz"
- dest: "{{ tcoffee_prefix }}/src/tcoffee/"
- creates: "{{ tcoffee_prefix }}/src/tcoffee/{{ tcoffee_version }}"
- copy: no
-
-
-- name: Creating directory in libexe
- file:
- path: "{{ tcoffee_prefix }}/libexec/tcoffee"
- state: directory
- mode: 0755
-
-
-- name: Copying executales in libexe dir
- command: cp -a "{{ tcoffee_prefix }}/src/tcoffee/{{ tcoffee_version }}/{{ item }}" "{{ tcoffee_prefix }}/libexec/tcoffee/"
- with_items:
- - bin
- - lck
- - mcoffee
- - methods
- - perl
- - plugins
-
-
-- name: Creating link to executable
- file:
- src: "{{ tcoffee_prefix }}/libexec/tcoffee/bin/t_coffee"
- dest: "{{ tcoffee_prefix }}/bin/t_coffee"
- state: link
-
-
-- name: Installing library required by t-coffee
- yum:
- name: ['libgfortran', 'argtable-devel']
- state: latest
-
-
-- name: Installing t-coffee third party software
- yum:
- name: ['gensoft-ClustalW-2.1', 'gensoft-mafft-7.310', 'gensoft-msaprobs-1.0.5', 'gensoft-muscle-3.8.31']
- state: latest
-
--
GitLab