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# Pjotr tasks
# Tags
* kanban: pjotrp
* assigned: pjotrp
* status: in progress
# Current
## 1U01HG013760
* Prefix-Free Parsing Compressed Suffix Tree (PFP) for tokenization
* Mempig
* [+] create backup server with @fredm
* [+] Moni builds 1U01HG013760
* [+] test framework wfmash - vertebrate tree and HPC compute?
* [ ] gbam - data compression with Nick and Hasithak
* [ ] accelerate wfmash with @santiago and team
* [ ] package wfmash and Rust wfa2-lib
* [ ] add Ceph for distributed network storage 1U01HG013760
* [ ] Work on pangenome genotyping 1U01HG013760
* [ ] update freebayes into Debian (version #)
* - [ ] static build and prepare for conda
* [ ] update vcflib into Debian (version #)
* - [ ] static build and prepare for conda
* [ ] pangenome as a 1st class input for GEMMA
* kilifish pangenome with Paul and Dario
* RAG with Shelby and Bonz
## Systems
* [ ] Backup production databases on Tux04
* - [ ] Dump redis
* - [ ] Dump sqlite
* - [ ] Dump mariadb
* [ ] make sure production is up to scratch (see stable below)
* [ ] synchronize git repos for public, CD, fallback and production using sheepdog and document
* [ ] drop tux02 backups on balg01
* [ ] drop backups in NL
* [ ] reintroduce borg-borg
* [X] Small database public
## Ongoing tasks (current/urgent)
* [ ] Precompute
* [+] Set up stable GeneNetwork server instance with new hardware (see below)
=> /topics/systems/fire-up-genenetwork-system-container.gmi
* [ ] Check email setup tux04
* [+] Julia as part of GN3 deployment
=> /topics/deploy/julia.gmi
# Tasks
## Meta-tasks
Now (X=done +=WIP _=kickoff ?=?)
* [ ] ~Test GEMMA/bulklmm speedups & paper
* [ ] GEMMA batch run and precompute
=> ../issues/gemma/lmm-precomputed-scores
* [ ] Genotyping and sparse VCF
* [ ] GeneNetwork consortium (paper & CTC)
* [+] Build leadership team
* [+] gBAM
* [ ] p-value global search
* [+] Xapian search add tags, notmuch style (with @bonfacem and @zachs)
=> ../issues/systems/octopus
* [+] Add R/qtl2 and multi-parent support with Karl (DO and Magic populations)
* [+] Fix slow search on Mariadb? Moving to xapian
* [.] GeneNetwork paper
* + [ ] add FAIR statement
* [ ] RISC-V trials
Longer term
* [ ] Drive for stability of GN tools (particularly GEMMA OOMP)
* [+] AraQTL and WormQTL2 embedding
* [+] Work on REST API
Later
* [ ] Mempang25 1U01HG013760
+ [ ] Invites
+ [ ] Payments
+ [ ] Rooms
+ [ ] Catering
* [ ] Remove ttf files GN2 git repo
* [+] DOI support GN
* [ ] Hao's idea for counting cis-qtl
* [ ] Improve search for significant and suggestive hits
* [ ] Include dominance matrix results in gemma (gene expression and transcript isophorms)
* [-] UCSC browser and big wig files (no longer applicable)
* [+] Jbrowse2 browser
### Set up stable server instance with new hardware
* [ ] ssh-shell access for git markdown
* [+] R/qtl2 with Karl and Alex, see [alex.gmi]
=> ./machine-room.gmi machine room
* [ ] 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
* [X] add drives to Octopus 1U01HG013760
* [X] mount NFS bacchus on octopus 1U01HG013760
* [X] Guix project server
* [X] Build junior team
* [X] Complete Octopus setup with Erik, Andrea and Efraim - adding all machines
* [X] Aging grant application w. Rob (fall)
* [X] Update facilities with new machines
* [X] Machine room security and access for bonz, fred, shelby, others...
* [X] Support pluto notebooks with Efraim
* [X] Frontend for GN4MSK
* [X] Test new caddy and drives
* [X] Set up cgit as a service
* [X] Fix mariadb index search - need to upgrade mariadb to convert final utf8mb4, see
=> ../issues/slow-sql-query-for-xapian-indexing.gmi
* [X] Debian/free software issues incl. vcflib work in Zig and release
* [X] Set up opensmtpd as a service
# 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
Generally work applies to NIH/R073237482 and other grants.
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