...
| Column |
|---|
|
| Code Block |
|---|
| language | bash |
|---|
| theme | Emacs |
|---|
| title | Terminal 1. Example SHPC Show command |
|---|
| $ 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 software packageaddition for mapping low-divergent sequences against
a large reference genome, such as the human genome.
latest:
bwa
latest:
0.7.15:17--h7132678_10: sha256:6f76c11a816b10440fd9d2c64c7183a31cc104a729f31a373c9b2b068138305ef9063141d8c5da87da76392b3a152b927b2913d47373f1874d76f14634b3f684
tags:
0.7.1517--h7132678_9: sha256:6f76c11a816b10440fd9d2c64c7183a31cc104a729f31a373c9b2b068138305e07822e4293a8c59755b295c448b9541db6c9bdbfdedb010bdbdcc1e1e935370f
v00.7.17--h7132678_cv110: sha256:9479b73e108ded3c12cb88bb4e918a5bf720d7861d6d8cdbb46d78a972b6ff1bf9063141d8c5da87da76392b3a152b927b2913d47373f1874d76f14634b3f684
aliasesdocker: quay.io/biocontainers/bwa
aliases:
bwa: /optusr/condalocal/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:
| Column |
|---|
|
| Code Block |
|---|
| language | bash |
|---|
| theme | Emacs |
|---|
| title | Terminal 2. Example SHPC Install command |
|---|
| $ 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--h7132678_10 was created.
Creating link $module_base/quay.io/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:
...
| Column |
|---|
|
| Code Block |
|---|
| language | bash |
|---|
| theme | Emacs |
|---|
| title | Terminal 3. Example SHPC module load |
|---|
| $ module avail bwa # search module
-------------------------------------------------------- /software/projects/ /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 BWA-MEM algorithm
fastmap identify super-maximal exact matches
pemerge memmerge overlapping paired ends (EXPERIMENTAL)
aln gapped/ungapped alignment
samse generate alignment 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'.
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.
|
|
| Note |
|---|
| title | Loading a module created by SHPC |
|---|
|
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.(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'.
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.
|
|
The full list of SHPC commands can be shown by using one of the help commands:
...