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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

• [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

Done