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| author | Pjotr Prins | 2023-12-03 09:35:19 -0600 |
|---|---|---|
| committer | Pjotr Prins | 2023-12-03 09:35:21 -0600 |
| commit | 42e6f37e9d1b0cf7d903dfdc4c5ee53fa625999d (patch) | |
| tree | ed3ceecb3233b87c55422756e06f82715087ffdf /topics/systems/mariadb | |
| parent | e03f2fa628cdc4d464c8e8b2cd185ec5a1880eb4 (diff) | |
| download | gn-gemtext-42e6f37e9d1b0cf7d903dfdc4c5ee53fa625999d.tar.gz | |
Notes on lizardfs
Diffstat (limited to 'topics/systems/mariadb')
| -rw-r--r-- | topics/systems/mariadb/precompute-mapping-input-data.gmi | 6 |
1 files changed, 6 insertions, 0 deletions
diff --git a/topics/systems/mariadb/precompute-mapping-input-data.gmi b/topics/systems/mariadb/precompute-mapping-input-data.gmi index caad794..12c21da 100644 --- a/topics/systems/mariadb/precompute-mapping-input-data.gmi +++ b/topics/systems/mariadb/precompute-mapping-input-data.gmi @@ -918,6 +918,12 @@ select * from StrainXRef WHERE InbredSetId=1 AND Used_for_mapping="Y" so it looks like we need some extra logic to fetch the used individuals from the actual genotype file(s). +For development I am running: + +``` +.guix-shell ruby --expose=/home/wrk/iwrk/opensource/code/genetics/gemma-wrapper/=/gemma-wrapper --expose=/home/wrk/iwrk/opensource/code/genetics/gemma/=/gemma -- guile -L . -s ./scripts/precompute/precompute-hits.scm +``` + ## Writing the phenotype file For gemma we need to feed a phenotype file that has only the individuals that are in the genotype file (the other 'missing' phenotype values should be NAs). |