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Add download to the help menu.

 - since this ocmmand is implemented already, it might as well
   be cited in the help menu

Signed-off-by: Sven-Thorsten Dietrich <sxd1425@miami.edu>
@thebigcorporation
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thebigcorporation commented Feb 19, 2022

`
Removing intermediate container 9fdba5e72613
---> 388cab128826
Successfully built 388cab128826
$ docker run -it 388cab128826 help
Usage:
epacts [command] [options]

 Command:
   help            Print out brief help message
   man             Print the full documentation in man page style
   single          Perform single variant association
   group           Perform groupwise (burden-style) association test
   anno            Annotate a VCF file
   zoom            Create a locus zoom plot from epacts results
   meta            Perform meta-analysis across multiple epacts results
   make-group      Create the group information for gene-based testing
   make-kin        Create a kinship matrix
   download        Download the reference sequence file
   version         prints version

 Visit http://genome.sph.umich.edu/wiki/EPACTS for more detailed documentation

$ docker run -it 388cab128826 download
Connecting to ftp.1000genomes.ebi.ac.uk
Downloading human_g1k_v37.fasta.fai..
Moving human_g1k_v37.fasta.fai to /usr/local/bin/..//share/EPACTS/
Downloading human_g1k_v37.fasta.gz.. Please be patient. This will take a while
Moving human_g1k_v37.fasta.gz to /usr/local/bin/..//share/EPACTS/
Decompressing the file
gzip -d /usr/local/bin/..//share/EPACTS/human_g1k_v37.fasta.gz

gzip: /usr/local/bin/..//share/EPACTS/human_g1k_v37.fasta.gz: decompression OK, trailing garbage ignored
Successfully installed the reference FASTA file`

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