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| author | Pjotr Prins | 2025-05-08 08:02:29 +0200 |
|---|---|---|
| committer | Pjotr Prins | 2025-05-08 08:02:35 +0200 |
| commit | 545f73daca01c67067cca606bda06da0c40b8cfd (patch) | |
| tree | 4c6819b0184474ca67f868258c01f81be30d8766 | |
| parent | 695fa00e927ac23f9b85bc9ed0e06072a2e33b06 (diff) | |
| download | gn-gemtext-545f73daca01c67067cca606bda06da0c40b8cfd.tar.gz | |
Pjotr tasks
| -rw-r--r-- | tasks/pjotrp.gmi | 15 | ||||
| -rw-r--r-- | topics/systems/mariadb/precompute-mapping-input-data.gmi | 13 |
2 files changed, 27 insertions, 1 deletions
diff --git a/tasks/pjotrp.gmi b/tasks/pjotrp.gmi index 5f8a620..5b95ebc 100644 --- a/tasks/pjotrp.gmi +++ b/tasks/pjotrp.gmi @@ -49,10 +49,23 @@ ## Ongoing tasks (current/urgent) * [ ] ~Felix, Alex, Rahul as friends of UTHSC -* [ ] Precompute +* [ ] Precompute with GEMMA + + [ ] Store N + + [ ] Store significance levels + + [ ] Check genotype input data + + [ ] Imputation + + [ ] Do same with bulkLMM + + [ ] Generate lmdb output + + [ ] Hook into Xapian + + [ ] Hook into correlations + * [ ] Check email setup tux04 * [ ] jbrowse plugin code - https://genenetwork.trop.in/mm10 * [+] bulklmm Julia as part of GN3 deployment + - precompute & Julia +=> https://github.com/GregFa/TestSysimage + Here the repo with BulkLMMSysimage: +=> https://github.com/GregFa/BulkLMMSysimage => /topics/deploy/julia.gmi * [X] Set up stable GeneNetwork server instance with new hardware (see below) => /topics/systems/fire-up-genenetwork-system-container.gmi diff --git a/topics/systems/mariadb/precompute-mapping-input-data.gmi b/topics/systems/mariadb/precompute-mapping-input-data.gmi index 24b052c..977120d 100644 --- a/topics/systems/mariadb/precompute-mapping-input-data.gmi +++ b/topics/systems/mariadb/precompute-mapping-input-data.gmi @@ -53,6 +53,19 @@ More recent incarnations are at v8, including a PublishData version that can be => https://github.com/genenetwork/genenetwork2/tree/testing/scripts/maintenance +Note that the locations are on space: + +``` +cd /mount/space2/lily-clone/acenteno/GN-Data +ls -l +python QTL_Reaper_v8_space_good.py 116 +-- +python UPDATE_Mean_MySQL_tab.py +cd /mount/space2/lily-clone/gnshare/gn/web/webqtl/maintainance +ls -l +python QTL_Reaper_cal_lrs.py 7 +``` + The first task is to prepare an update script that can run a set at a time and compute GEMMA output (instead of reaper). The script first fetches inbredsets |