Pjotr tasks

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)
[ ] 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

[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:

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