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SHPC is used by Pawsey staff to deploy some of the available scientific softwares, in particular bioinformatics applications.

Using SHPC

Installing a container for a software included in the SHPC registry requires no knowledge of containers and Singularity: all you need are the software name and version.

The key commands of SHPC are show and install; let's see them in action with an example. Suppose we want to install the bioinformatics package BWA. We can use the shpc show command to browse the SHPC registry of available containers:

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Versions installed in Pawsey systems

To check the current installed versions, use the module avail command (current versions may be different from content shown here):

$ module loadavail shpc/0.1.28  # load SHPC module

$ shpc show -f bwa  # search for a package in SHPC registry (string search)
biocontainers/bwa
ghcr.io/autamus/bwa

$ shpc show biocontainers/bwa  # inspect specific container recipe
docker: biocontainers/bwa
url: https://hub.docker.com/r/biocontainers/bwa
maintainer: '@vsoch'
description: BWA is a software package for mapping low-divergent sequences against
  a large reference genome, such as the human genome.
latest:
  0.7.15: sha256:6f76c11a816b10440fd9d2c64c7183a31cc104a729f31a373c9b2b068138305e
tags:
  0.7.15: sha256:6f76c11a816b10440fd9d2c64c7183a31cc104a729f31a373c9b2b068138305e
  v0.7.17_cv1: sha256:9479b73e108ded3c12cb88bb4e918a5bf720d7861d6d8cdbb46d78a972b6ff1b
aliases:
  bwa: /opt/conda
------------------------------------ /software/setonix/2024.05/pawsey/modules -------------------------------------
   shpc/0.1.28

Using SHPC

Installing a container for a software included in the SHPC registry requires no knowledge of containers and Singularity: all you need are the software name and version.

The key commands of SHPC are show and install; let's see them in action with an example. Suppose we want to install the bioinformatics package BWA. We can use the shpc show command to browse the SHPC registry of available containers:

$ module load shpc/<VERSION>  # load SHPC module with the correct version

$ shpc show -f bwa  # search for a package in SHPC registry (string search)
quay.io/biocontainers/bwa
ghcr.io/autamus/bwa

$ shpc show quay.io/biocontainers/bwa  # inspect specific container recipe
docker: biocontainers/bwa
url: https://biocontainers.pro/tools/bwa
maintainer: '@vsoch'
description: shpc-registry automated BioContainers addition for bwa
latest:
0.7.17--h7132678_10: sha256:f9063141d8c5da87da76392b3a152b927b2913d47373f1874d76f14634b3f684
tags:
0.7.17--h7132678_9: sha256:07822e4293a8c59755b295c448b9541db6c9bdbfdedb010bdbdcc1e1e935370f
0.7.17--h7132678_10: sha256:f9063141d8c5da87da76392b3a152b927b2913d47373f1874d76f14634b3f684
docker: quay.io/biocontainers/bwa
aliases:
bwa: /usr/local/bin/bwa

The information of interest in this output is the list of available versions (or tags), in this case: 0.7.15 and v0.7.17_cv1. Let's install the former:

$ shpc install quay.io/biocontainers/bwa:0.7.1517--h7132678_10
singularity pull --name /software/projects/projectcodepawsey0001/rsrchrbuser/setonix/containers2024.05/containers/sif/quay.io/biocontainers/bwa/0.7.15/17--h7132678_10/quay.io-biocontainers-bwa-0.7.1517--h7132678_10-sha256:6f76c11a816b10440fd9d2c64c7183a31cc104a729f31a373c9b2b068138305ef9063141d8c5da87da76392b3a152b927b2913d47373f1874d76f14634b3f684.sif docker://quay.io/biocontainers/bwa@sha256:6f76c11a816b10440fd9d2c64c7183a31cc104a729f31a373c9b2b068138305ef9063141d8c5da87da76392b3a152b927b2913d47373f1874d76f14634b3f684
INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
Getting image
source signatures

[..]

INFO:    Creating SIF file...
Module quay.io/software/projects/projects/projectcode/rsrchr/setonix/containers/sif/biocontainers/bwa:0.7.17--h7132678_10 was created.
Creating link $module_base/quay.io/biocontainers/bwa/0.7.15/biocontainers-bwa-0.7.15-sha256:6f76c11a816b10440fd9d2c64c7183a31cc104a729f31a373c9b2b068138305e.sif
Module biocontainers/bwa:0.7.15 was created.17--h7132678_10/module.lua -> $views_base/modules/bwa/0.7.17--h7132678_10.lua

That's it!

By default SHPC downloads containers under:

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$ module avail bwa  # search module

----------- /software/projects/projectcode/rsrchr/setonix/2024.05/containers/views/modules -------------
   bwa/0.7.17--h7132678_10 

$ module load biocontainers/bwa/0.7.15/module  # load module

$ bwa  # test command

Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.17-r1188
Contact: Heng Li <lh3@sanger.ac.uk>

Usage: bwa <command> [options]

Command: index index sequences in the FASTA format
mem BWA-MEM algorithm
fastmap identify super-maximal exact matches
pemerge merge overlapping paired ends (EXPERIMENTAL)
aln gapped/ungapped alignment
samse generate alignment (single ended)
sampe generate alignment (paired ended)
bwasw BWA-SW for long queries

shm manage indices in shared memory
fa2pac convert FASTA to PAC format
pac2bwt generate BWT from PAC
         pac2bwtgen    alternative algorithm for generating BWT
    
    bwtupdate     update .bwt to the new format
        
bwt2sa        generate SA from BWT and Occ

Note: To use BWA, you need to first index the genome with `bwa index'.
      index'.
There are three alignment algorithms in BWA: `mem', `bwasw', and
      `aln/samse/sampe'. If you are not sure which to use, try `bwa mem'
      first. Please `man ./bwa.1' for the manual.

 `man ./bwa.1' for the manual.

The full list of SHPC commands can be shown by using one of the help commands:

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$ module load shpc/0.1.28<VERSION>  # load SHPC module

$ shpc show -f velvet
$

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