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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

[+] 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

Later

[ ] Hao's idea for counting cis-qtl
[ ] 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
[ ] tux01 has unused 4TB spinning disk
[ ] tux02 has unused 2x4TB spinning disks and 2TB nvme /dev/nvme0n1 on adapter

https://www.cyberciti.biz/faq/upgrade-update-samsung-ssd-firmware/

apt-get install fwupd fwupdate

fwupdmgr get-devices

fwupdmgr update

The previously problematic Samsung 980 Pro was basically using the 3B2QGXA7, and now Samsung has introduced a new 5B2QGXA7 firmware to fix the problem. The problem mainly affects the 2TB version of the 980 Pro

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] NSF report with UTHSC
[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