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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
~/opt/guix-pull/bin/guix shell guile guile-dbi guile-json -- guile -L . -e main -s scripts/precompute/run-gemma.scm 115476.json
and with some extra paths (for gemma)
~/opt/guix-pull/bin/guix shell -C -F xz python python-lmdb tar time parallel coreutils-minimal guile guile-dbi guile-json ruby --expose=/home/wrk/iwrk/opensource/code/genetics/gemma-wrapper/=/gemma-wrapper --expose=/home/wrk/iwrk/opensource/code/genetics/gemma/=/gemma -- env TMPDIR=tmp GEMMA_COMMAND=/gemma/bin/gemma-0.98.5-linux-static-debug guile -L . -e main -s ./scripts/precompute/run-gemma.scm --id 21529
!#
(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))
(id (value #t))
(help (single-char #\h) (value #f))))
(options (getopt-long args option-spec))
(show-version (option-ref options 'version #f))
(help-wanted (option-ref options 'help #f))]
(if show-version
(begin
(display "run-gemma version 1.0\n")
(exit)))
(if help-wanted
(format #t "run-gemma
Usage: run-gemma [options...] filename(s)
--id Run on identifier
-v --version Display version
-h --help Display this help
")
(let* [(trait-id (option-ref options 'id "0"))
(trait-fn (string-append trait-id ".json"))
]
(call-with-input-file trait-fn
(lambda (port)
(let* [(json (json->scm port))
(dataset (car (assoc-ref json "data")))
(data (cdr dataset))
(dataset-name (assoc-ref data "name"))
(trait-name (assoc-ref data "trait-name"))
(traits (assoc-ref data "traits"))
(pheno-fn (string-append trait-id "-pheno.txt"))
]
(write-pheno-file pheno-fn traits)
(invoke-gemma-wrapper-loco dataset-name trait-name trait-fn pheno-fn "BXD.8_geno.txt.gz")
)))))))
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