# 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

* [+] 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

=> ./dana.gmi 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:
=> 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] 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
* [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