From 545f73daca01c67067cca606bda06da0c40b8cfd Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 8 May 2025 08:02:29 +0200
Subject: Pjotr tasks

---
 tasks/pjotrp.gmi                                         | 15 ++++++++++++++-
 topics/systems/mariadb/precompute-mapping-input-data.gmi | 13 +++++++++++++
 2 files changed, 27 insertions(+), 1 deletion(-)

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
-- 
cgit v1.2.3