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| Code Block |
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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/modules ---------------------------------------------------------
biocontainers/bwa/0.7.15/module
$ module load biocontainers/bwa/0.7.15/module # 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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| 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. |
The full list of SHPC commands can be shown by using one of the help commands:
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