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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

• [ ] NSF report with UTHSC
• [+] Shelby's application and biosketch
• [.] Check Tony's list and improve search for SNPs and Hs
• [.] GeneNetwork paper
• [ ] Machine room security and access for bonz, fred, shelby, others...
• [ ] Set up student VM
• [.] Tree of life

• [ ] Check backups of etc etc.
• [ ] GeneNetwork consortium
• [+] Machine room HDDs
• [ ] Byron epigenetics paper

Later

• [ ] Batch run GEMMA and faster file handling
• [ ] Run any2any alignments of pathogens
• [ ] Improve search for significant and suggestive hits
• [ ] GEMMA speedups
• [ ] Aging studies
• [ ] RISC-V
• [+] DOI support GN (Paris)
• [ ] Automate tux01 restart for GN2+GN3 services

Ongoing tasks

See Dan's list for machine room

• [ ] VPN access and FoUT
• [ ] DMZ plan
• [ ] Setup VM on Tux02
• [ ] Key 410H
• [ ] research.gov submit Postdoc plan
• [+] Complete vcflib work in Zig and release
• [+] Reinstate backup drops on tux02, rabbit, &space and &epysode; reduce incoming IP
• [+] Order drives and caddies tux01 & tux02 (with @haoc)
• [+] Guix and Julia with Gregory
• [ ] Check Adrian's compiler w. odgi
• [ ] Update mars (fallback machine) also for development
• [ ] Pluto tool with Zach & Efraim
• [+] Introduce &disk space and mdstat monitor
• [+] run sheepdog as root: redis password error; introduce SHEEPDOG_CONF
• [ ] 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

• [X] Write test for R/qtl, GEMMA and other mapping
• [X] Fix https on tux01
• [X] Fix Lily edit form

http://gn1.genenetwork.org/infoshare/manager/member-studies-edit.html?DatasetId=101

• [X] Opar.io move to dnsimple
• [X] Run tux01 backups serially
• [X] Add tux02 to rabbit's sheepdog
• [X] Get status list from sheepdog on epysode, tux02 and rabbit on GN2
• [X] Add accounts Erik, Andrea, Hao to P2
• [X] Add accounts Bonz, Fred, Alex to tux02
• [X] Restart luna
• [X] Fix genecup errors (with @efraimf)
• [X] Copy database to space (space3 dir) (@arthurc)
• [X] Output sheepdog monitor