README.md

phylogenie machines

The machines installation recipe for the pasteur phylogny course . The recipes are based on ansible. It also use gensoft yum repository then it will work for hosts operating CentOS6.

The installed packages are:

• beast
• beagle
• bmge
• clustaO
• clustalW
• fastme
• FigTree
• IQ-TREE
• goalign
• gotree
• jmodeltest2
• lsd
• mafft
• mrbayes
• msaprobs
• muscle
• palm
• raxml
• raxml-ng
• seaview
• tracer
• tempest
• pastml

and

• the libreoffice suite
• vim
• emacs
• xemacs
• nano
• gedit
• firefox
• wget and curl

how to deploy a new machine

clone the project

`git clone git@gitlab.pasteur.fr:bneron/phylogeny-machines.git`
or
`https://gitlab.pasteur.fr/bneron/phylogeny-machines.git`

install ansible

The framework used to install the host is ansible. So if you are not familiar with it, please check the ansible documentation.
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

Tell to ansible the hosts to deploy

vim Inventory/hosts
[phylogeny]
157.99.191.140

then run it

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 practices.yml then add option -t <tag> then run

ansible-playbook  --limit phylogeny -u formateur --ask-pass --become -t editors phylogeny.yml

how to install a new soft

from a gensoft package

If the software is packaged in gensoft repository (http://mirrors.web.pasteur.fr/gensoft/) just add an item in the gensoft_packs dict located Inventory/group_vars/all file.

• name: is the name of the gensoft package.
• vers: is the package version.

from sources

You have to write a new role and add it in the phylogeny.yml playbook and play the role

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 But if your soft is not installed via gensoft you have to write a rule to add it in menu by your self.

• pack_name: is the name of the gensoft package.
• bin_name: is the name of the binary to launch.
• vers: is the package version.
• term: is true if the binary need a terminal to be launch. false otherwise.

then play the tag menu

ansible-playbook  -t menu phylogeny.yml

if it's a new gensoft package run the entire role gensoft:

ansible-playbook  -t gensoft phylogeny.yml