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| author | Pjotr Prins | 2024-08-03 14:00:09 +0200 |
|---|---|---|
| committer | Pjotr Prins | 2024-08-03 14:00:09 +0200 |
| commit | 591dd752274dd4530040b272fb0c0513a2ce203d (patch) | |
| tree | e8c377209fe246d26699aba426203acf1a912f30 /scripts/precompute/run-gemma.scm | |
| parent | 51048dfd4cc16352b9d5e615ad24e1510141f141 (diff) | |
| download | gn-guile-591dd752274dd4530040b272fb0c0513a2ce203d.tar.gz | |
precompute: pass in trait id for gemma
Diffstat (limited to 'scripts/precompute/run-gemma.scm')
| -rwxr-xr-x | scripts/precompute/run-gemma.scm | 8 |
1 files changed, 5 insertions, 3 deletions
diff --git a/scripts/precompute/run-gemma.scm b/scripts/precompute/run-gemma.scm index 00cc68d..4952834 100755 --- a/scripts/precompute/run-gemma.scm +++ b/scripts/precompute/run-gemma.scm @@ -9,7 +9,7 @@ Run from base dir with 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 test +~/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 !# @@ -30,6 +30,7 @@ and with some extra paths (for gemma) ;; (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)) @@ -41,11 +42,12 @@ and with some extra paths (for gemma) (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 "115475") - (trait-fn "115475.json") + (let* [(trait-id (option-ref options 'id "0")) + (trait-fn (string-append trait-id ".json")) ] (call-with-input-file trait-fn |