TARA User Guide
- TARA User Guide
- Overview of TARA
- File Storage and transfer
- How to Use Application System
- Compiling Source Code
- Introduction to SLURM
- Running Jobs by SLURM Script
- Running Jobs by SLURM Interactive
- Singularity
- ThaiSC Support
- Frequently Asked Questions (FAQ)
Singularity
Singularity is a containers has the following steps.
- Install Singularity version 3.x in your computer (Linux) by following steps in https://sylabs.io/guides/3.6/user-guide/quick_start.html
- Pull docker image for you want to use. Ex. This command for pull Anaconda2 from https://hub.docker.com/r/continuumio/anaconda2
singularity pull docker://continuumio/anaconda2
- Build sandbox in singularity for install your software. By use command.
sudo singularity build --sandbox FunGAP_snabox/ anaconda2_latest.sif
- Shell to singularity sandbox and use writable mode for install software.
sudo singularity shell --writable FunGAP_snabox/
**Notice If you can see Singularity> when You’re into container environment.
- Install software in singularity container
conda update conda
conda config --remove channels bioconda
conda config --remove channels conda-forge
conda config --add channels bioconda/label/cf201901
conda config --add channels conda-forge/label/cf201901
conda install augustus rmblast maker hisat2 braker busco=3.0.2 blast pfam_scan bowtie2
- When install software complete, exit for singularity container by command.
exit
- Buid .sif file for use on TARA HPC (get FunGAP.sif)
sudo singularity build FunGAP.sif FunGAP_snabox/
- Transfer FunGAP.sif to TARA HPC. On TARA HPC, You use singularity by command.
module load Singularity #call module Singularity
singularity exec FunGAP.sif <command> #execute container