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Unverified Commit cbb988e1 authored by Bertrand  NÉRON's avatar Bertrand NÉRON
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:bug: fix role tempest

tempest download page is not esaly scriptable => I provide the src
fix the copying files in libexe path
parent d2f4a80a
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---
- name: Set tcoffee prefix
set_fact:
tcoffee_prefix: /usr/local
tcoffee_version: T-COFFEE_installer_Version_13.39.0.d675aed_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
File added
...@@ -2,28 +2,30 @@ ...@@ -2,28 +2,30 @@
- name: Set tempest prefix - name: Set tempest prefix
ansible.builtin.set_fact: ansible.builtin.set_fact:
tempest_prefix: /usr/local tempest_prefix: /usr/local
tempest_version: '1.5.3' tempest_PN: TempEst
tempest_version: 'v1.5.3'
- name: Install java - name: Install java
ansible.builtin.apt: ansible.builtin.apt:
name: openjdk-17-jdk name: openjdk-17-jdk
state: latest state: latest
- name: Creating dir source for t-coffee - name: Creating source directory for tempest
ansible.builtin.file: ansible.builtin.file:
path: "{{ tempest_prefix }}/src/tempest" path: "{{ tempest_prefix }}/src/tempest"
state: directory state: directory
- name: download tempest - name: Copy Tempest archive to remote
ansible.builtin.get_url: # the fucking tempest page is not easily scriptable (coockie on so on)
url: "http://tree.bio.ed.ac.uk/download.html?name=tempest&id=102&num=3" ansible.builtin.copy:
dest: "{{ tempest_prefix }}/src/tempest" src: archive/TempEst_v1.5.3.tgz
dest: "{{ tempest_prefix }}/src/tempest/TempEst_v1.5.3.tgz"
- name: Unarchive tempest - name: Unarchive tempest
ansible.builtin.unarchive: ansible.builtin.unarchive:
src: "{{ tempest_prefix }}/src/tempest/{{ tempest_version }}.tar.gz" src: "{{ tempest_prefix }}/src/tempest/{{ tempest_PN}}_{{ tempest_version }}.tar.gz"
dest: "{{ tempest_prefix }}/src/tempest" dest: "{{ tempest_prefix }}/src/tempest"
creates: "{{ tempest_prefix }}/src/tempest/{{ tempest_version }}" creates: "{{ tempest_prefix }}/src/tempest/{{ tempest_PN}}_{{ tempest_version }}"
copy: no copy: no
- name: Creating directory in libexe - name: Creating directory in libexe
...@@ -33,8 +35,13 @@ ...@@ -33,8 +35,13 @@
mode: '0755' mode: '0755'
- name: Copying executables in libexe dir - name: Copying executables in libexe dir
ansible.builtin.command: cp -a "{{ tempest_prefix }}/src/tempest/{{ tempest_version }}/{{ item }}" "{{ tempest_prefix }}/libexec/tempest/" # ansible package with ubuntu:focal is 2.9.6
with_items: # instead as it show in online doc 2.9
# command is not in ansible.builtin.
# if use ansible.builtin.command
# we have the CRYPTIC error "no command given"
command: cp -a "{{ tempest_prefix }}/src/tempest/{{ tempest_PN}}_{{ tempest_version }}/{{ item }}" "{{ tempest_prefix }}/libexec/tempest/"
loop:
- bin - bin
- images - images
- lib - lib
......
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