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| language | bash |
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| theme | Emacs |
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| title | Terminal 2. Example SHPC Install command |
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| $ shpc install biocontainers/bwa:0.7.15
singularity pull --name /software/projects/projectcode/rsrchr/shpcsetonix/containers/sif/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/projects/projectcode/rsrchr/shpcsetonix/containers/sif/biocontainers/bwa/0.7.15/biocontainers-bwa-0.7.15-sha256:6f76c11a816b10440fd9d2c64c7183a31cc104a729f31a373c9b2b068138305e.sif
Module biocontainers/bwa:0.7.15 was created. |
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That's it! When modulefile paths are configured appropriately in the system (shell logout/login may be required the first time), you
By default SHPC downloads containers under:
/software/projects/<project-id>/<user-name>/setonix/containers/sif/
and creates modulefiles under:
/software/projects/<project-id>/<user-name>/setonix/containers/modules/
You are able to use module avail, module load, and module unload: (as these are system modules, note the slash "/" for the version, instead of the colon ":" above for the tags):
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| language | bash |
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| title | Terminal 3. Example SHPC module load |
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| $ module avail bwa # search module
-------------------------------------------------------- /software/projects/projectcode/rsrchr/shpcsetonix/containers/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.
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