$ shpc show -f velvet  # can SHPC locate the new recipe? yes!
quay.io/biocontainers/velvet

$ shpc install quay.io/biocontainers/velvet:1.2.10--h5bf99c6_4  # installing Velvet
singularity pull --name /software/projectcode/rsrchr/shpc/containers/quay.io/biocontainers/velvet/1.2.10--h5bf99c6_4/quay.io-biocontainers-velvet-1.2.10--h5bf99c6_4-sha256:7fc2606a1431883dcd0acf830abcfeddb975677733d110a085da0f07782f5a27.sif docker://quay.io/biocontainers/velvet@sha256:7fc2606a1431883dcd0acf830abcfeddb975677733d110a085da0f07782f5a27
INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
Getting image source signatures

[..]

INFO:    Creating SIF file...
/software/projects/projectcode/rsrchr/shpc/containers/quay.io/biocontainers/velvet/1.2.10--h5bf99c6_4/quay.io-biocontainers-velvet-1.2.10--h5bf99c6_4-sha256:7fc2606a1431883dcd0acf830abcfeddb975677733d110a085da0f07782f5a27.sif
Module quay.io/biocontainers/velvet:1.2.10--h5bf99c6_4 was created.

$ module load quay.io/biocontainers/velvet/1.2.10--h5bf99c6_4/module  # loading module

$ velvetg --help  # testing a command
Usage:
./velvetg directory [options]

	directory			: working directory name

Standard options:
	-cov_cutoff <floating-point|auto>	: removal of low coverage nodes AFTER tour bus or allow the system to infer it
		(default: no removal)
	-ins_length <integer>		: expected distance between two paired end reads (default: no read pairing)
	-read_trkg <yes|no>		: tracking of short read positions in assembly (default: no tracking)
	-min_contig_lgth <integer>	: minimum contig length exported to contigs.fa file (default: hash length * 2)
	-amos_file <yes|no>		: export assembly to AMOS file (default: no export)
	-exp_cov <floating point|auto>	: expected coverage of unique regions or allow the system to infer it
		(default: no long or paired-end read resolution)
	-long_cov_cutoff <floating-point>: removal of nodes with low long-read coverage AFTER tour bus
		(default: no removal)

Advanced options:
	-ins_length* <integer>		: expected distance between two paired-end reads in the respective short-read dataset (default: no read pairing)
	-ins_length_long <integer>	: expected distance between two long paired-end reads (default: no read pairing)
	-ins_length*_sd <integer>	: est. standard deviation of respective dataset (default: 10% of corresponding length)
		[replace '*' by nothing, '2' or '_long' as necessary]
	-scaffolding <yes|no>		: scaffolding of contigs used paired end information (default: on)
	-max_branch_length <integer>	: maximum length in base pair of bubble (default: 100)
	-max_divergence <floating-point>: maximum divergence rate between two branches in a bubble (default: 0.2)
	-max_gap_count <integer>	: maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)
	-min_pair_count <integer>	: minimum number of paired end connections to justify the scaffolding of two long contigs (default: 5)
	-max_coverage <floating point>	: removal of high coverage nodes AFTER tour bus (default: no removal)
	-coverage_mask <int>	: minimum coverage required for confident regions of contigs (default: 1)
	-long_mult_cutoff <int>		: minimum number of long reads required to merge contigs (default: 2)
	-unused_reads <yes|no>		: export unused reads in UnusedReads.fa file (default: no)
	-alignments <yes|no>		: export a summary of contig alignment to the reference sequences (default: no)
	-exportFiltered <yes|no>	: export the long nodes which were eliminated by the coverage filters (default: no)
	-clean <yes|no>			: remove all the intermediary files which are useless for recalculation (default : no)
	-very_clean <yes|no>		: remove all the intermediary files (no recalculation possible) (default: no)
	-paired_exp_fraction <double>	: remove all the paired end connections which less than the specified fraction of the expected count (default: 0.1)
	-shortMatePaired* <yes|no>	: for mate-pair libraries, indicate that the library might be contaminated with paired-end reads (default no)
	-conserveLong <yes|no>		: preserve sequences with long reads in them (default no)

Output:
	directory/contigs.fa		: fasta file of contigs longer than twice hash length
	directory/stats.txt		: stats file (tab-spaced) useful for determining appropriate coverage cutoff
	directory/LastGraph		: special formatted file with all the information on the final graph
	directory/velvet_asm.afg	: (if requested) AMOS compatible assembly file