Page Comparison

$ module load shpc/0.0.53  # 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

$ shpc install biocontainers/bwa:0.7.15
singularity pull --name /software/projectcode/rsrchr/shpc/containers/biocontainers/bwa/0.7.15/biocontainers-bwa-0.7.15-sha256:6f76c11a816b10440fd9d2c64c7183a31cc104a729f31a373c9b2b068138305e.sif docker://biocontainers/bwa@sha256:6f76c11a816b10440fd9d2c64c7183a31cc104a729f31a373c9b2b068138305e
INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
Getting image source signatures

[..]

INFO:    Creating SIF file...
/software/projects/projectcode/rsrchr/shpc/containers/biocontainers/bwa/0.7.15/biocontainers-bwa-0.7.15-sha256:6f76c11a816b10440fd9d2c64c7183a31cc104a729f31a373c9b2b068138305e.sif
Module biocontainers/bwa:0.7.15 was created.

$ module avail bwa  # search module

-------------------------------------------------------- /software/projectcode/rsrchr/shpc/modules ---------------------------------------------------------
   biocontainers/bwa/0.7.15/module

$ module load biocontainers/bwa/0.7.15  # load module

$ bwa  # test command

Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.15-r1140
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'.
      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.

$ module load shpc/0.0.53  # load SHPC module

$ shpc show -f velvet
$

$ shpc config get registry  # get registry location
registry                       /software/projects/projectcode/rsrchr/shpc/registry

# create directory tree for desired Velvet container recipe
$ mkdir -p /software/projects/projectcode/rsrchr/shpc/registry/quay.io/biocontainers/velvet

# create a new YAML container recipe in the new path (using vi as text editor here)
$ vi /software/projects/projectcode/rsrchr/shpc/registry/quay.io/biocontainers/velvet/container.yaml

docker: quay.io/biocontainers/velvet

latest:
  "1.2.10--h5bf99c6_4": "sha256:7fc2606a1431883dcd0acf830abcfeddb975677733d110a085da0f07782f5a27"
tags:
  "1.2.10--h5bf99c6_4": "sha256:7fc2606a1431883dcd0acf830abcfeddb975677733d110a085da0f07782f5a27"
  "1.2.10--hed695b0_3": "sha256:b17fd98d802c1e78dde5fd2c5431efc1969db35a279f3a5ca7afcb46efc66e4a"

maintainer: "@marcodelapierre"

# these are optional
description: "Velvet is a sequence assembler for short reads."
url: https://quay.io/repository/biocontainers/velvet

aliases:
  velvetg: /usr/local/bin/velvetg
  velveth: /usr/local/bin/velveth