diff options
| -rw-r--r-- | tasks/pjotrp.gmi | 51 |
1 files changed, 33 insertions, 18 deletions
diff --git a/tasks/pjotrp.gmi b/tasks/pjotrp.gmi index 936fd01..e5e25fe 100644 --- a/tasks/pjotrp.gmi +++ b/tasks/pjotrp.gmi @@ -6,15 +6,28 @@ * 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). +# Current -=> https://issues.genenetwork.org +## 1U01HG013760 -Generally work applies to NIH/R073237482 and other grants. +* Prefix-Free Parsing Compressed Suffix Tree (PFP) for tokenization +* Mempig -# Current +* [+] 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 @@ -23,12 +36,11 @@ Generally work applies to NIH/R073237482 and other grants. * - [ ] Dump sqlite * - [ ] Dump mariadb * [ ] make sure production is up to scratch (see stable below) -* [ ] Small database public * [ ] synchronize git repos for public, CD, fallback and production using sheepdog and document -* [ ] add Ceph for distributed network storage 1U01HG013760 * [ ] drop tux02 backups on balg01 -* [ ] drop backups NL +* [ ] drop backups in NL * [ ] reintroduce borg-borg +* [X] Small database public ## Ongoing tasks (current/urgent) @@ -38,8 +50,6 @@ Generally work applies to NIH/R073237482 and other grants. * [ ] Check email setup tux04 * [+] Julia as part of GN3 deployment => /topics/deploy/julia.gmi -* [ ] Work on pangenome genotyping 1U01HG013760 -* [+] Moni builds 1U01HG013760 # Tasks @@ -56,11 +66,11 @@ Now (X=done +=WIP _=kickoff ?=?) * [+] Build leadership team * [+] gBAM * [ ] p-value global search -* [+] Xapian search add tags, notmuch style (with @zachs) +* [+] 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) +* [+] 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 @@ -91,11 +101,7 @@ Later ### Set up stable server instance with new hardware * [ ] ssh-shell access for git markdown -* [ ] R/qtl2 with Karl and Alex -* [+] Set up opensmtpd as a service - + [ ] Add package dependency - + [X] Test on open port 25 - + [ ] Add public-inbox (Arun) +* [+] R/qtl2 with Karl and Alex, see [alex.gmi] => ./machine-room.gmi machine room @@ -123,3 +129,12 @@ Later * [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. |