summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
-rw-r--r--issues/systems/octopus.gmi21
-rw-r--r--tasks/machine-room.gmi4
-rw-r--r--tasks/pjotrp.gmi26
3 files changed, 35 insertions, 16 deletions
diff --git a/issues/systems/octopus.gmi b/issues/systems/octopus.gmi
index bc421eb..c510fd9 100644
--- a/issues/systems/octopus.gmi
+++ b/issues/systems/octopus.gmi
@@ -1,20 +1,27 @@
# Octopus sysmaintenance
+Reopened tasks because of new sheepdog layout and add new machines to Octopus and get fiber optic network going with @andreag. See also
+
+=> ../../topics/systemtopics/systems/hpcs/hpc/octopus-maintenance
+
# Tags
-* assigned: pjotrp, efraimf, erikg
+* assigned: pjotrp, efraimf, erikg, andreag
* priority: high
-* status: completed, closed
+* status: open
* type: system administration
* keywords: systems, octopus
# Tasks
-* [X] install sheepdog
-* [X] run borg backup
-* [X] propagate backup to rabbit
-* [X] fix redis updates - use rev tunnel
-* [X] check other dirs
+* [ ] add lizardfs to nodes
+* [ ] add PBS to nodes
+* [ ] use fiber optic network
+* [ ] install sheepdog
+* [ ] run borg backup
+* [ ] propagate backup to rabbit
+* [ ] fix redis updates - use rev tunnel
+* [ ] check other dirs
# Info
diff --git a/tasks/machine-room.gmi b/tasks/machine-room.gmi
index 03905f6..c0e61d1 100644
--- a/tasks/machine-room.gmi
+++ b/tasks/machine-room.gmi
@@ -11,6 +11,8 @@
### UTHSC
+* [ ] fix www.genenetwork.org and gn2.genenetwork.org https
+* [ ] tux02 certbot failing
* [ ] get data from summer211.uthsc.edu (access machine room)
* [ ] VPN access and FoUT
* [ ] penguin2 has 32TB of space we can use on NFS/backups
@@ -55,8 +57,10 @@ Security:
* [ ] Run GN off balg01
* [X] Firewall out of band
+* [ ] Add firewall test to sheepdog
* [X] Add storage
* [ ] Convert balg02 to Guix server
+* [ ] VM for student team
### Done
diff --git a/tasks/pjotrp.gmi b/tasks/pjotrp.gmi
index c99bf6e..1c42fcb 100644
--- a/tasks/pjotrp.gmi
+++ b/tasks/pjotrp.gmi
@@ -19,34 +19,42 @@ The tasks here should probably be broken out into appropriately tagged issues, w
Now (X=done +=WIP _=kickoff ?=?)
* [+] Build leadership team
-* [+] Build junior team
+* [X] Build junior team
* [+] Build GN consortium
* [+] gBAM
+* [+] Set up stable GeneNetwork server instance with new hardware (see below)
* [ ] Complete Octopus setup with Erik, Andrea and Efraim - adding all machines
+* [ ] p-value global search
+
+=> ../issues/systems/octopus
+
* [ ] GEMMA batch run and precompute
-* [ ] GEMMA/bulklmm speedups
-* [+] Set up stable GeneNetwork server instance with new hardware (see below)
-* [ ] Drive for stability of GN tools (particularly GEMMA OOMP)
-* [+] Work on REST API
-* [+] AraQTL and WormQTL2 embedding
+=> ../issues/gemma/lmm-precomputed-scores
+
+* [ ] GEMMA/bulklmm speedups
* [ ] Add R/qtl2 and multi-parent support with Karl (DO and Magic populations)
* [ ] Fix slow search on Mariadb?
-* [+] Aging grant application w. Rob (fall)
* [+] Shelby's application (fall)
* [.] GeneNetwork paper
* + [ ] add FAIR statement
* [ ] RISC-V trials
* [ ] Guix project server
+Longer term
+
+* [+] Aging grant application w. Rob (fall)
+* [ ] Drive for stability of GN tools (particularly GEMMA OOMP)
+* [+] AraQTL and WormQTL2 embedding
+* [+] Work on REST API
+
Later
+* [+] DOI support GN
* [+] Tree of life w. Andrea
* [ ] Hao's idea for counting cis-qtl
* [ ] Improve search for significant and suggestive hits
-* [+] DOI support GN (Barcelona)
-* [ ] Cito support (Barcelona)
* [ ] Include dominance matrix results in gemma (gene expression and transcript isophorms)
* [ ] UCSC browser and big wig files
* [ ] Jbrowse2 browser