This is a repository for scripts and recipes to install software on ilifu. The list of software managed here can be seen below
These installations can be found in the ansible directory.
Configure the locations for software in the file: ansible/group_vars/all. The structure of the file looks something like:
---
software_root: /software
data_root: /software/data
astro_dir: "{{ software_root }}/astro"
astro_container_dir: "{{ astro_dir }}/containers"
astro_container_recipe_dir: "{{ astro_container_dir }}/recipes"
astro_src: "{{ astro_dir }}/src"
astro_data_dir: "{{ data_root }}/astro"
bio_dir: "{{ software_root }}/bio"
bio_container_dir: "{{ bio_dir }}/containers"
bio_container_recipe_dir: "{{ bio_container_dir }}/recipes"
bio_src: "{{ bio_dir }}/src"
bio_data_dir: "{{ data_root }}/bio"
common_dir: "{{ software_root }}/common"
common_container_dir: "{{ common_dir }}/containers"
common_container_recipe_dir: "{{ common_container_dir }}/recipes"
common_src: "{{ common_dir }}/src"
modules_dir: "{{ software_root }}/modules"
astro_modules: "{{ modules_dir }}/astro"
bio_modules: "{{ modules_dir }}/bio"
common_modules: "{{ modules_dir }}/common"
admin_group: "idia-admins"
singularity: "/software/common/singularity/4.1.0/bin/singularity"where software_root is probably the most important variable to configure — this is the root directory where all software will be installed. Please also remember to configure the location of your singularity install in the singularity variable.
This is a reasonably typical ansible installation. Note that EVERYTHING is disabled by default apart from configuring the directories, which is ALWAYS run. There are typically two classes of software that can be installed: compiled software; and containers. While installation is similar for both, installing containers does require root access (via sudo) if the container is built from a recipe.
So to install, say openmpi 4.0.3, one would run the command: ansible-playbook site.yaml -t openmpi,openmpi4.0.3. Note that both the software name tag and the version-specific tag (comma-separated, e.g., openmpi,openmpi4.0.3) are required due to the loop structure. Software to be installed needs to be explicitly tagged, otherwise it will be ignored. Installation of the specific software will also install the appropriate environment module (lmod) in ${software_root}/modules.
Note that your user will need sudo rights in order to build containers.
The repository contains over 200 software packages across three categories. All software requires explicit tagging and is disabled by default. Installation requires both the software name tag and the version-specific tag (e.g., python,python3.12.8 or samtools,samtools1.22.1).
| Software | Available Versions | ansible tag (example) | module name |
|---|---|---|---|
| Python | 2.7.18, 3.6-3.13.2 | python,python3.12.8 | python/3.12.8 |
| R | 4.0.0-4.4.1 | R,R4.4.1 | R/4.4.1 |
| OpenMPI | 2.1.1-5.0.3 | openmpi,openmpi5.0.3 | openmpi/5.0.3 |
| CUDA | 10.0-12.4.0 | cuda,cuda12.4.0_550.54.14 | cuda/12.4.0_550.54.14 |
| Singularity | 2.6.1-4.1.3 | singularity,singularity4.1.3 | singularity/4.1.3 |
| Go | 1.16.3-1.22.4 | golang,golang1.22.4 | golang/1.22.4 |
| Julia | 1.5.3, 1.10.4 | julia,julia1.10.4 | julia/1.10.4 |
| .NET | 2.1-8.0 | dotnet,dotnet8.0.301 | dotnet/8.0.301 |
| Anaconda | 2020.07-2024.10 | anaconda,anaconda2024.10 | anaconda/2024.10 |
| Software | Available Versions | ansible tag (example) | module name |
|---|---|---|---|
| SAMtools | 1.10-1.22.1 | samtools,samtools1.22.1 | samtools/1.22.1 |
| BCFtools | 1.10.2-1.22 | bcftools,bcftools1.22 | bcftools/1.22 |
| GATK | 4.2.5.0-4.5.0.0 | gatk,gatk4.5.0.0 | gatk/4.5.0.0 |
| BWA | latest | bwa,bwa | bwa/latest |
| BLAST+ | 2.15.0, 2.16.0 | blast,blast2.16.0 | blast/2.16.0 |
| FastQC | 0.11.9, 0.12.1 | fastqc,fastqc0.12.1 | fastqc/0.12.1 |
| MultiQC | 1.13-1.22.3 | multiqc,multiqc1.22.3 | multiqc/1.22.3 |
| STAR | 2.7.11b | star,star2.7.11b | star/2.7.11b |
| VEP | 101.0, 106.1 | vep,vep106.1 | vep/106.1 |
| Minimap2 | 2.24 | minimap2,minimap22.24 | minimap2/2.24 |
| Software | Version/Type | ansible tag |
|---|---|---|
| RStudio | Various R versions | RStudio,RStudio2025.05.1-513-R4.5.1 |
| Spectronaut | 20.0 | spectronaut,spectronaut20.0 |
| DIA-NN | 1.8.1 | diann,diann1.8.1 |
| Beast | 1.10.4 | beast,beast1.10.4 |
| ClinSV | 1.0.0 | ClinSV,ClinSV1.0.0 |
| PopGen Suite | 0.1 | popgen,popgen0.1 |
| Software | Available Versions | ansible tag (example) | module name |
|---|---|---|---|
| cfitsio | 3.450, 4.3.1 | cfitsio,cfitsio4.3.1 | cfitsio/4.3.1 |
| calceph | 2.3.2 | calceph,calceph2.3.2 | calceph/2.3.2 |
For a complete list of available software and versions, check the task files in ansible/roles/*/tasks/.