From 9708991177a8450f8c17dad732f35a4b9c95c287 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 27 Jun 2024 05:29:26 -0500 Subject: Simplified gemma runner --- scripts/precompute/run-gemma.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'scripts/precompute') 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") )))))) -- cgit v1.2.3