HPC Bioinfomatics Software Stack

How we add packages in jubail

We added packages in below methods.

  • Installed via easybuild ( eg:- module load samtools/1.9 )

  • Installed via conda environment ( eg:- source activate /scratch/gencore/conda3/envs/repeatmasker4.1.5 )

  • Installed via compiling from source ( eg:- Using the tar.gz of the package )

  • Installed via singularity in jubail ( this is still experimental )

  • Installed via Docker on our annotation server.

Loading package using conda

This section explains how to load modules under gencore/2.

To load gencore2 modules

$ module load all
$ module load gencore/2
  1. Specify the first two letter of the software, and hit tab twice and you may able to see the options of software.

    In the below example, I searched for samtools package, I entered first two letter and hit tab button twice

$ module load sa
  salmon/    samtools/  savage/

  1. Good, now I can see there is a module for samtools under gencore/2. If you find the package and then to check if you require any specific version of samtools, again issue tab button twice, you are able to see the versions.

$ module load samtools/
  samtools/1.3.1  samtools/1.9

  1. Great, now I can choose samtools module with version 1.3.1

$ module load samtools/1.3.1

  1. To check the loaded modules in your current shell

$ module list

Loading package using “source activate <package-path>”

This section explains how to load packages under conda. In the below example, using Miniconda module, you are enabling the repeatmasker 4.1.5 verison as a conda environment on your path.

$ module load gencore/1
$ module load Miniconda3/4.7.10
$ source activate /scratch/gencore/conda3/envs/repeatmasker4.1.5

Loading package from sources

This section explains how to load packages source path location. Compiled packages are available under below path.

$ /scratch/gencore/software/

To load the specified package path, for eg:- maker version 2, you may issue below command in your command line.

$ export PATH='/scratch/gencore/software/maker2':$PATH

To request a package

If you unable to find a package, you may proceed with sending an email to nyuad.cgsb.cb@nyu.edu by mentioning below pointers.

  • Software version

  • Github or Software download link

  • If required databases to be downloaded, specify the exact link, names etc…