ThaiSC

Singularity

TARA User Guide

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