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authorPjotr Prins2025-05-08 08:02:29 +0200
committerPjotr Prins2025-05-08 08:02:35 +0200
commit545f73daca01c67067cca606bda06da0c40b8cfd (patch)
tree4c6819b0184474ca67f868258c01f81be30d8766
parent695fa00e927ac23f9b85bc9ed0e06072a2e33b06 (diff)
downloadgn-gemtext-545f73daca01c67067cca606bda06da0c40b8cfd.tar.gz
Pjotr tasks
-rw-r--r--tasks/pjotrp.gmi15
-rw-r--r--topics/systems/mariadb/precompute-mapping-input-data.gmi13
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