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| author | Pjotr Prins | 2024-07-11 12:14:06 +0200 |
|---|---|---|
| committer | Pjotr Prins | 2024-07-11 12:14:06 +0200 |
| commit | b03f0ada0c3e64c16eeba4278d0b8a4470a26b10 (patch) | |
| tree | 2285d7f1d3215ea57c208f1dc9868cda569b71ea /scripts/precompute | |
| parent | 84a85da3d4934d43c3caf5cefb660e0d5aaec6f4 (diff) | |
| download | gn-guile-b03f0ada0c3e64c16eeba4278d0b8a4470a26b10.tar.gz | |
Handle genotype filename to pass into gemma-wrapper
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 9a7bba2..b0db622 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 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 +~/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 !# @@ -54,5 +54,5 @@ Usage: list-traits-to-compute [options...] (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) + (invoke-gemma-wrapper-loco dataset-name trait-name trait-fn pheno-fn "BXD.8_geno.txt.gz") )))))) |