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SHPC is used by Pawsey staff to deploy some of the available scientific softwares, in particular bioinformatics applications.
Versions installed in Pawsey systems
To check the current installed versions, use the module avail command:
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| language | bash |
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| theme | DJango |
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| title | Terminal 1. Checking for installed versions |
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| $ module avail shpc
------------------------------------ /software/setonix/2024.05/pawsey/modules -------------------------------------
shpc/0.1.28 |
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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.
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| language | bash |
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| title | Terminal 1. Example SHPC Show command |
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| $ module load shpc/0.1.28<VERSION> # 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/bin/bwa
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| language | bash |
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| title | Terminal 4. Velvet not on SHPC registry |
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| $ module load shpc/0.1.28<VERSION> # load SHPC module
$ shpc show -f velvet
$ |
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