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| author | Pjotr Prins | 2024-06-27 05:29:26 -0500 |
|---|---|---|
| committer | Pjotr Prins | 2024-06-27 05:29:26 -0500 |
| commit | 9708991177a8450f8c17dad732f35a4b9c95c287 (patch) | |
| tree | 97ef69d53150ecd2700f77277b134480390facd6 /scripts/precompute | |
| parent | e4775ccc0c24351e1ee428cddb0f320022509137 (diff) | |
| download | gn-guile-9708991177a8450f8c17dad732f35a4b9c95c287.tar.gz | |
Simplified gemma runner
Diffstat (limited to 'scripts/precompute')
| -rwxr-xr-x | scripts/precompute/run-gemma.scm | 4 |
1 files changed, 2 insertions, 2 deletions
diff --git a/scripts/precompute/run-gemma.scm b/scripts/precompute/run-gemma.scm index 36edf8b..48222b4 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) -. .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 +guix shell -C -F xz tar time parallel gemma 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 guile -L . -e main -s ./scripts/precompute/run-gemma.scm test !# @@ -49,5 +49,5 @@ Usage: list-traits-to-compute [options...] ] (display dataset) (write-pheno-file "pheno.txt" traits) - ; (run-gemma "BXD" data-id probeset-id probesetfreeze-id name trait-name traits))) + (invoke-gemma-wrapper-loco dataset-name trait-name "pheno.txt") )))))) |