Might be helpful to point out in your Readme that on a Mac, it will be necessary to switch to using gnu getopt instead of the default getopt in order for your dbgap-docker.bash script to run. This can be done by issuing these commands:
brew install gnu-getopt
brew link --force gnu-getopt
With the default version of getopt that comes with the Macs, the dbgap-docker.bash example commands dies with this rather cryptic error message:
$ ./dbgap-docker.bash -i ./input_files/1000_Genomes_Study/ -o ./output_files/1000_Genomes_Study -m ./input_files/1000_Genomes_Study/metadata.json up
getopt: illegal option -- l
getopt: illegal option -- g
getopt: illegal option -- e
getopt: illegal option -- l
getopt: illegal option -- ,
getopt: illegal option -- u
getopt: illegal option -- :
getopt: illegal option -- ,
getopt: illegal option -- u
getopt: illegal option -- u
getopt: illegal option -- :
getopt: illegal option -- ,
getopt: illegal option -- a
Wrong number/type of arguments
Usage: dbgap-docker.bash [-h] [-i, --input [input directory]]
[-o, --output [output directory]]
[-m, --manifest [manifest file]]
[up|down]
The above pull request #19 provides a work-around by detecting macOS and forcing the script to only attempt to use the short options supported by BSD's getopt.
Might be helpful to point out in your Readme that on a Mac, it will be necessary to switch to using gnu getopt instead of the default getopt in order for your
dbgap-docker.bash
script to run. This can be done by issuing these commands:With the default version of getopt that comes with the Macs, the
dbgap-docker.bash
example commands dies with this rather cryptic error message: