Summary

This page covers information on how to use the new 'Pawsey Bio - Ubuntu 20.04 - 2021-11' image for Nimbus. Instructions on how to choose this image when creating your instance can be found here. This Bio-image is created to cater to bioinformatics users who prefer to have their instances pre-installed with software commonly used in the bioinformatics domain. Some of the software are part of Pawsey's ongoing effort to improve the experience of bioinformatics users at Pawsey.

Before you begin

You may be required to input your SSH public key or the path to your SSH public key on your local machine while using some of these software. Please ensure you have it ready to go. Instructions for how to generate one can be found /wiki/spaces/SUP/pages/55410887.

Commonly used software

Instructions

On this page, we will cover instructions for how to use CernVM-FS and Singularity-HPC. For instructions for other software listed above, please see the links provided above, or the software's original documentation page.

CernVM-FS

CernVM-FS is a read-only file system that was developed by another supercomputing centre (Cern). It allows files such as container tools, reference datasets and other shared resources that are commonly used by many researchers to be accessed, added to, and updated in the one location. At Pawsey, we currently cache the Biocontainer tools and reference genome datasets that are on Galaxy Project's repositories. Please note that the data sets may not be comprehensive, and this service is not meant to replace your current methods for accessing public datasets.

sudo apt-get autoremove cvmfs
sudo apt-get purge cvmfs
sudo rm -rf /etc/cvmfs/
git clone https://github.com/PawseySC/Pawsey-CernVM-FS.git
cd Pawsey-CernVM-FS
sudo ./install-cvmfs.sh install

Then, to access and view the entire list of Biocontainer tools from the repository: 

Note: It may take a minute or two to load the folders. When you have done it once, it will not take as long to show again.

The /cvmfs/singularity.galaxyproject.org/all subdirectory is where the entire list of 8000+ Biocontainers can be found, with the alphabetical subdirectories being symlinks to them.

$ ls -la /cvmfs/singularity.galaxyproject.org
total 140
drwxr-xr-x 33 cvmfs cvmfs 4096 Mar 25  2020 .
drwxr-xr-x  3 cvmfs cvmfs 4096 May 12  2022 1
drwxr-xr-x  3 cvmfs cvmfs 4096 Jun 29  2020 2
drwxr-xr-x  4 cvmfs cvmfs 4096 Feb 10 07:09 3
drwxr-xr-x 24 cvmfs cvmfs 4096 Feb 23  2021 a
drwxr-xr-x  4 cvmfs cvmfs 4096 Mar  7 19:06 all
drwxr-xr-x 23 cvmfs cvmfs 4096 Sep  2  2022 b
drwxr-xr-x 26 cvmfs cvmfs 4096 Feb 10 15:05 c
drwxr-xr-x 22 cvmfs cvmfs 4096 Feb 10 15:05 d
drwxr-xr-x 23 cvmfs cvmfs 4096 May  1  2020 e
drwxr-xr-x 21 cvmfs cvmfs 4096 Feb 10 19:06 f
drwxr-xr-x 25 cvmfs cvmfs 4096 Feb  5  2022 g
drwxr-xr-x 19 cvmfs cvmfs 4096 Feb 10 21:21 h
drwxr-xr-x 18 cvmfs cvmfs 4096 Feb 10 21:21 i
drwxr-xr-x 14 cvmfs cvmfs 4096 Jul 10  2020 j
drwxr-xr-x 21 cvmfs cvmfs 4096 Feb 25  2021 k
drwxr-xr-x 16 cvmfs cvmfs 4096 Feb 10 22:54 l
drwxr-xr-x 26 cvmfs cvmfs 4096 Feb 10 22:54 m
drwxr-xr-x 20 cvmfs cvmfs 4096 Feb 11 05:13 n
drwxr-xr-x 14 cvmfs cvmfs 4096 May  7  2020 o
drwxr-xr-x 24 cvmfs cvmfs 4096 Aug 24  2021 p
drwxr-xr-x 12 cvmfs cvmfs 4096 Feb 27  2021 q
drwxr-xr-x 27 cvmfs cvmfs 4096 Jun 28  2022 r
drwxr-xr-x 26 cvmfs cvmfs 4096 Apr  7  2020 s
drwxr-xr-x 24 cvmfs cvmfs 4096 Feb 11 23:17 t
drwxr-xr-x 13 cvmfs cvmfs 4096 Feb 11 23:17 u
drwxr-xr-x 18 cvmfs cvmfs 4096 Feb 11 23:17 v
drwxr-xr-x 17 cvmfs cvmfs 4096 Jul 28  2021 w
drwxr-xr-x 16 cvmfs cvmfs 4096 Apr  7  2020 x
drwxr-xr-x  4 cvmfs cvmfs 4096 Feb 28  2021 y
drwxr-xr-x 10 cvmfs cvmfs 4096 Feb 11 23:17 z

To access the data files:

$ ls -la /cvmfs/data.galaxyproject.org/
total 14
drwxr-xr-x   4 cvmfs cvmfs 4096 Mar 31  2016 .
-rw-r--r--   1 cvmfs cvmfs   21 Oct 24  2018 .cvmfsdirtab
drwxr-xr-x 210 cvmfs cvmfs 4096 Apr 21  2022 byhand
drwxr-xr-x  18 cvmfs cvmfs 4096 Nov 24  2020 managed

To use these data files for your analyses, copy the absolute file path in your workflow/pipeline. For example, with the reference genome Hg38, the file can be found in the following location, and specifically under the seq sub directory:

$ ls -la /cvmfs/data.galaxyproject.org/byhand/hg38
total 46
drwxrwxr-x  10 cvmfs cvmfs 4096 Apr 22  2016 .
drwxr-xr-x 210 cvmfs cvmfs 4096 Apr 21  2022 ..
-rw-r--r--   1 cvmfs cvmfs    0 Apr 22  2016 .cvmfscatalog
drwxrwxr-x   3 cvmfs cvmfs 4096 Jan 21  2015 download
drwxrwxr-x   6 cvmfs cvmfs 4096 Jan 20  2015 hg38canon
drwxrwxr-x   6 cvmfs cvmfs 4096 Jan 20  2015 hg38female
drwxrwxr-x   6 cvmfs cvmfs 4096 Jan 20  2015 hg38full
drwxrwxr-x   2 cvmfs cvmfs 4096 Mar 18  2014 liftOver
drwxrwxr-x   2 cvmfs cvmfs 4096 Mar 18  2014 picard_index
drwxrwxr-x   2 cvmfs cvmfs 4096 Mar 18  2014 sam_index
drwxrwxr-x   2 cvmfs cvmfs 4096 Apr  1  2016 seq


$ ls -la /cvmfs/data.galaxyproject.org/byhand/hg38/seq
total 10108046
drwxrwxr-x  2 cvmfs cvmfs       4096 Apr  1  2016 .
drwxrwxr-x 10 cvmfs cvmfs       4096 Apr 22  2016 ..
-rw-rw-r--  1 cvmfs cvmfs        136 Mar 18  2014 README
-rw-rw-r--  1 cvmfs cvmfs  835393456 Mar 18  2014 hg38.2bit
lrwxrwxrwx  1 cvmfs cvmfs         11 May 17  2014 hg38.fa -> hg38full.fa
-rw-r--r--  1 cvmfs cvmfs      19327 Aug 24  2015 hg38.fa.fai
-rw-rw-r--  1 cvmfs cvmfs 3150052305 Mar 17  2014 hg38canon.fa
-rw-rw-r--  1 cvmfs cvmfs 3091680335 Mar 17  2014 hg38female.fa
-rw-r--r--  1 cvmfs cvmfs        757 Apr  1  2016 hg38female.fa.fai
-rw-rw-r--  1 cvmfs cvmfs 3273481150 Mar 18  2014 hg38full.fa

So the full absolute path for the Hg38 sequence file would be:

/cvmfs/data.galaxyproject.org/byhand/hg38/seq/hg38full.fa

sudo apt-get autoremove cvmfs
sudo apt-get purge cvmfs
sudo rm -rf /etc/cvmfs/
git clone https://github.com/PawseySC/Pawsey-CernVM-FS.git
cd Pawsey-CernVM-FS
sudo ./install-cvmfs.sh install

Singularity-HPC

Singularity-HPC is a software for container modules. If you are familiar with using containers, this is an added bonus to your experience in using containers. If you are not, this is a great way to start using containers. As container syntax can be messy and confusing, being able to use them as modules removes the need for using container syntaxes. Singularity-HPC was created by one of the original developers of Singularity, and the registry includes many bioinformatics containers that can be readily pulled and used. 

Before you begin, ensure to move your containers folder to your storage volume (.i.e. /data), then update the container base path:

mv /home/ubuntu/containers /data/containers
shpc config set container_base:/data/containers

To see the entire list of containers available on the registry, run the following command:

shpc list 

At Pawsey, we recommend using S-HPC's registry of quay.io/biocontainers containers, as Biocontainers are a reliable source of well-built containers, with versions that are seamlessly matched to BioConda's tools. To narrow down the list to biocontainers, run:

shpc show -f quay.io/biocontainers

To install any of these containers, run:

shpc install quay.io/biocontainers/TOOL_NAME

To use installed containers, run the following and use the tool as you normally would (no container syntax required):

module load quay.io/biocontainers/TOOL_NAME

Notes:

• The list in the registry is not exhaustive, more packages are being added each day by the community
• Pawsey is working to add to the quay.io/biocontainers list successively

• You may want to reclone the repo so that your list is always updated, as such:

  git clone https://github.com/singularityhub/singularity-hpc
  sudo mv /singularity-hpc /shpc