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#! Run GEMMA
A simple script that takes the JSON input from list-traits-to-compute and runs
GEMMA on those.
Run from base dir with
guix shell guile guile-dbi -- guile -L ../.. -s run-gemma.scm --help
and with some extra paths
. .guix-shell ruby --expose=/home/wrk/iwrk/opensource/code/genetics/gemma-wrapper/=/gemma-wrapper --expose=/home/wrk/iwrk/opensource/code/genetics/gemma/=/gemma -- env TMPDIR=tmp guile -L . -s ./scripts/precompute/run-gemma.scm
!#
(use-modules ; (gn data dataset)
; (gn data hits)
; (gn data strains)
; (gn util convert)
(gn runner gemma)
(ice-9 getopt-long)
(ice-9 match)
(ice-9 textual-ports)
(json)
(rnrs bytevectors)
(srfi srfi-1)
)
(define (main args)
;; (write args)
(let* [
(option-spec '( (version (single-char #\v) (value #f))
(help (single-char #\h) (value #f))))
(options (getopt-long args option-spec))
(help-wanted (option-ref options 'help #f))]
(if help-wanted
(format #t "list-traits-to-compute writes JSON traits files from the GN DB
Usage: list-traits-to-compute [options...]
-h, --help Display this help
")
(display "gemma-run")
)))
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