blob: 69fbdfb73cdb21374772b7f48408846cf521db4e (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
|
# Pjotr tasks
## Tags
* kanban: pjotrp
* assigned: pjotrp
* status: in progress
## Notes
The tasks here should probably be broken out into appropriately tagged issues, where they have not - they can be found and filtered out with tissue (formerly gnbug).
=> https://issues.genenetwork.org
## Tasks
### Meta-tasks
Now
* [ ] Set up stable GeneNetwork server instance with new hardware (see below)
* [ ] Work on REST API
* [ ] GN4MSK rebranding - see issue
* [ ] Fix slow search on Mariadb
* [ ] Drive for stability of GN tools (particularly GEMMA OOMP)
* [ ] GEMMA batch run and precompute
* [ ] GEMMA/bulklmm speedups
* [ ] Add R/qtl2 and multi-parent support with Karl
* [ ] Support pluto notebooks with Efraim
* [ ] Aging grant application w. Rob (August)
* [+] Shelby's application (fall)
* [.] GeneNetwork paper
* + [ ] add FAIR statement
* [ ] RISC-V trials
* [ ] gBAM
Later
* [.] Tree of life w. Andrea
* [+] Machine room security and access for bonz, fred, shelby, others...
* [ ] Hao's idea for counting cis-qtl
* [ ] Improve search for significant and suggestive hits
* [+] DOI support GN (Paris)
* [ ] Cito support
### Ongoing tasks
### Set up stable server instance with new hardware
* [+] Create bootable Debian drive that uses ttyS0
* [ ] Pluto with Efraim
* [ ] R/qtl2 with Karl
* [ ] Set up opensmtpd as a service
+ [ ] Add package dependency
+ [ ] Test on open port 25
+ [ ] Add public-inbox
* [ ] Test new caddy and drives
* [ ] Set up cgit as a service
=> ./machine-room.gmi machine room
* [X] Fix mariadb index search - need to upgrade mariadb to convert final utf8mb4, see
=> ../issues/slow-sql-query-for-xapian-indexing.gmi
* [+] move backup dirs on tux01 to a larger partition (from export3 to export2)
* [ ] Frontend for GN4MSK
* [.] Check Tony's list and improve search for SNPs and Hs
* [ ] GeneNetwork consortium (paper & CTC)
* [ ] Key 410H
* [ ] research.gov submit Postdoc plan
* [+] Complete vcflib work in Zig and release
* [ ] Fix issues:
=> https://genenetwork.org/show_trait?trait_id=10441&dataset=HSNIH-PalmerPublish slow mapping
=> http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=2
* [ ] Fix GN1 uploader:
=> ../issues/genenetwork1/gn1-production-system-issues.gmi
* [ ] fix GN1 images linking to http://www.webqtl.org/array_images/S238-1F1-U74Av2.png
### Done
|
