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| language | bash |
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| theme | Emacs |
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| title | Terminal 1. Example SHPC Show command |
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| $ 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://hubbiocontainers.docker.com/r/biocontainerspro/tools/bwa
maintainer: '@vsoch'
description: BWAshpc-registry isautomated aBioContainers softwareaddition packagefor forbwa
mapping low-divergent sequences against
a large reference genome, such as the human genome.
latest:
latest:
0.7.17--h7132678_10: sha256:f9063141d8c5da87da76392b3a152b927b2913d47373f1874d76f14634b3f684
tags:
0.7.17--h7132678_9: sha256:07822e4293a8c59755b295c448b9541db6c9bdbfdedb010bdbdcc1e1e935370f
0.7.1517--h7132678_10: sha256:6f76c11a816b10440fd9d2c64c7183a31cc104a729f31a373c9b2b068138305ef9063141d8c5da87da76392b3a152b927b2913d47373f1874d76f14634b3f684
tagsdocker: 0.7.15: sha256:6f76c11a816b10440fd9d2c64c7183a31cc104a729f31a373c9b2b068138305e
v0.7.17_cv1: sha256:9479b73e108ded3c12cb88bb4e918a5bf720d7861d6d8cdbb46d78a972b6ff1b
aliases:
bwa: /opt/conda/bin/bwa
quay.io/biocontainers/bwa
aliases:
bwa: /usr/local/bin/bwa
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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:
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| language | bash |
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| title | Terminal 2. Example SHPC Install command |
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| $ shpc install quay.io/biocontainers/bwa:0.7.1517--h7132678_10
singularity pull --name /software/projects/projectcodepawsey0001/rsrchrbuser/setonix/2024.05/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...
/software/projects/projects/projectcode/rsrchr/setonix/containers/sif/
Module quay.io/biocontainers/bwa/:0.7.15/biocontainers17-bwa-0.7.15-sha256:6f76c11a816b10440fd9d2c64c7183a31cc104a729f31a373c9b2b068138305e.sif
Module biocontainers/bwa:0.7.15 was created.-h7132678_10 was created.
Creating link $module_base/quay.io/biocontainers/bwa/0.7.17--h7132678_10/module.lua -> $views_base/modules/bwa/0.7.17--h7132678_10.lua |
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That's it!
By default SHPC downloads containers under:
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| language | bash |
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| theme | Emacs |
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| title | Terminal 3. Example SHPC module load |
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| $ module avail bwa # search module
-------------------------------------------------------- /software/projects/projectcode/rsrchr/setonix/containers /software/projects/projectcode/rsrchr/setonix/2024.05/containers/views/modules ---------------------------------------------------------
biocontainers/bwa/0.7.15/module
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: 0.7.1517-r1140r1188
Contact: Heng Li <lh3@sanger.ac.uk>
Usage: bwa <command> [options]
Command: index index sequences in the FASTA format
mem 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 alngenerate alignment (paired ended)
bwasw BWA-SW for long queries
shm gapped/ungappedmanage alignmentindices in shared memory
fa2pac convert FASTA to PAC format
samsepac2bwt generate BWT from PAC
pac2bwtgen alternative algorithm for generategenerating alignmentBWT
(singlebwtupdate ended)update .bwt to the new format
bwt2sa generate SA from sampeBWT and Occ
Note: To use BWA, you generateneed alignmentto (pairedfirst ended)index the genome with `bwa index'.
There are three alignment bwaswalgorithms in BWA: `mem', `bwasw', and
`aln/samse/sampe'. If you BWA-SWare fornot longsure querieswhich to use, try `bwa mem'
first. Please `man ./bwa.1' for 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'.
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.
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| Note |
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| title | Loading a module created by SHPC |
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As of version 0.0.53 of SHPC, modules created using this tool require the suffix /module to be loaded correctly. For instance: module load biocontainers/bwa/0.7.15/module
Failing to add the /module will result in an error, and no module will be loaded. This behaviour is going to be improved in future SHPC versions.
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The full list of SHPC commands can be shown by using one of the help commands:
...