- GeneNetwork Releases
document created 23 hours ago by Frederick Muriuki Muriithi
The tagging of the commits will need to distinguish repository-specific tags from overall system tags.
In this document, we only concern ourselves with the overall system tags, that shall have...
- Using curl
document created on Dec 23 2022 by Pjotr Prins
..."2310010I16Rik"
sheepdog_run.rb -c "curl \"$URL\"|grep -i $FIND" --tag "wild-card-search-$URL" $*
```
## POST fetch
Post fetches are a bit harder. First use firefox console and click of Debugger tab.
- Backup Drops
document created on Oct 27 2022 by Pjotr Prins, last updated 25 hours ago by Pjotr Prins
...-v --tag "drop-mount-dropserver" -c "sshfs -o IdentityFile=~/.ssh/id_ecdsa_backup bacchus@dropserver:/ ~/mnt/this"
sheepdog_run.rb -h rabbit --always -v --tag "drop-rsync-dropserver" -c "rsync -vrltDP...
- CI/ CD for genetwork projects
document created on Oct 12 2022 by Munyoki Kilyungi, last updated 2 weeks ago by Pjotr Prins
...reuse container from staging; tag container as a release container
* Deploy container to production
* Generate documentation for tagged commit
* Generate guix declaration for re-generating the release...
- GeneNetwork CLI
document created on Sep 20 2021 by jgart, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...CLI
## Tags
* assigned: ??
* type: feature-request
* priority: low
* keywords: command-line interface, CLI
## Description
It would be great for GeneNetwork to have a nice command line client for doing...
- Add button to delete an entire dataset in gn2
document created on Sep 08 2021 by BonfaceKilz, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...delete an entire dataset in gn2
## Tags
* assigned: ??
* type: bug
* keywords: ui, dangerous feature, status: unclear
## Description
An interface for deleting data existed in gn1 but is not present in...
- Using pudb
document created on Dec 21 2021 by jgart, last updated on Dec 03 2023 by Pjotr Prins
...interface
> as Python’s built-in pdb module. Just replace pdb with pudb. (One
> exception: run is called runstatement.)
=> https://docs.python.org/3/library/pdb.html?highlight=pdb#module-pdb
## Tags...
- Running pudb From an External Environment
document created on Dec 03 2023 by Pjotr Prins
...--load=guix.scm
4) Inside the container, run the debugger with something like:
* env PYTHONPATH="${PYTHONPATH}:${HOME}/pudb_env/lib/python3.8/site-packages" ... python3 -m pudb script.py
## Tags...
- Using pudb with pytest
document created on Dec 21 2021 by jgart, last updated on Dec 03 2023 by Pjotr Prins
Using pudb with pytest
```
pytest --pdbcls pudb.debugger:Debugger --pdb --capture=no
```
=> https://documen.tician.de/pudb/starting.html?highlight=pytest#usage-with-pytest
## Tags...
- Profiling Python code
document created on Dec 03 2023 by Pjotr Prins
...e.g.
* env [various-env-vars] python3 -m cProfile the-script.py 2>error.log 1>performance.log
which should help will separating errors from the performance data, for easier analysis
## Tags...
- Jupyter notebooks
document created on Sep 01 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...notebooks
## Tags
* type: documentation
* keywords: documentation, jupyter, notebooks
* status: unclear
## Run with GNU Guix
Jupyter notebooks can be installed in a profile
```
~/opt/guix-latest/bin/...
- LMM Notes
document created on Aug 13 2021 by Pjotr Prins, last updated on Jan 08 2024 by Solomon Shelby
...Tags
* assigned: ??
* keywords: LMM
* status: unclear
* priority: low
## Time series data
FlxQTL by Saunak Sen can handle time series data in an (genetic) LMM
context. They have to be measured...
- Defining a scheme sexp comment with a reader macro
document created on Feb 02 2022 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...-character #\# #\; (lambda (s c n) c n (read s t nil t) (values)))
CL-USER(2): (+ 3 (+ 2 3) 1)
9
CL-USER(3): (+ 3 #;(+ 2 3) 1)
4
```
Special thanks to Ed Langley on #common-lisp:matrix.org.
## Tags...
- Debugging Lisp
document created on Dec 22 2021 by Pjotr Prins, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...provided by Common Lisp
Some links
=> https://malisper.me/debugging-lisp-part-1-recompilation/ Debug Common Lisp (CL)
=> https://www.youtube.com/watch?v=bl8jQ2wRh6k Video on CL web development
## Tags...
- Common LISP: sly
document created on Jan 29 2022 by Pjotr Prins, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Common LISP: sly
This document will collect some resources on sly
## Tags
* type: documentation
* keywords: common-lisp, sly, emacs
## Resources
=> https://joaotavora.github.io/sly/ SLY User Manual
- Common LISP: Notes
document created on Feb 09 2022 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...com/nonguix/nonguix/-/blob/master/nongnu/packages/emacs.scm#L26 clhs
## Getting Help / Asking Questions
### Libera Chat
```
#clschool
#commonlisp
```
### Matrix
```
#common-lisp:matrix.org
```
## Tags...
- Non-Clustered and Flippable Heatmaps
document created on Oct 01 2021 by Frederick Muriuki Muriithi, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...be possible to flip the heatmap orientation from horizontal to vertical and vice-versa
* It should be possible to generate a heatmap with no dendrograms
## Members
* fredm
* pjotr
* zsloan
## Tags...
- Indicating Heterozygosity
document created on Jun 20 2024 by Frederick Muriuki Muriithi, last updated on Jun 20 2024 by Frederick Muriuki Muriithi
Indicating Heterozygosity
## Tags
* status: ongoing
* assigned: fredm, zachs, acenteno
* type: documentation
* priority: medium
* keywords: doc, documentation, heterozygous, hererozygosity...
- Genome Details
document created on Jul 01 2024 by Frederick Muriuki Muriithi
...know where this fits
## Tags
* type: documentation, doc, docs
* assigned: fredm
* priority: docs
* status: open
* keywords: gn-uploader, uploader, genome
## Location
### centiMorgan (cM)
We no longer...
- Genenetwork Streaming Functionality
document created 5 weeks ago by Alexander_Kabui
...Tags
* type: documentation
* Keywords: documentation, docs, genenetwork, streaming
### Introduction
Genenetwork implements streaming functionality that logs results from a running external process...
- Ideas and References
document created on Nov 22 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Ideas and References
=> gemini://drewdevault.com/2021/11/15/Reframing-gemini.gmi Reframing the philosophy of Gemini
## Tags
* type: documentation
* keywords: documentation, gemini
- gemtext cheatsheet
document created on Dec 21 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
gemtext cheatsheet
=> gemini://gemini.circumlunar.space/docs/cheatsheet.gmi
=> https://gemini.circumlunar.space/docs/cheatsheet.gmi proxy
## Tags
* type: documentation
* keywords: gemini
- GeneNetwork documentation
document created on Nov 16 2021 by Pjotr Prins, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
.../gn-docs/blob/master/general/help/facilities.md
the markdown is rendered on github, which makes it easy to edit for most users, so it should be the default.
## Tags
* assigned: pjotrp
* status: unclear...
- Deploy GeneNetwork
document created on Jan 18 2023 by Arun Isaac, last updated on Aug 27 2024 by Frederick Muriuki Muriithi
...Tags
* type: doc, docs, documentation
* keywords: deploy, deployment, deploying, guix, guix container, guix system container
* status: in progress
# Description
This page attempts to document...
- Data Uploads: Reversing a Diff
document created on Feb 03 2022 by BonfaceKilz, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...Reversing a Diff
## Tags
* assigned: bonfacem, zachs
* status: unclear
* type: enhancement
* priority: high
* keywords: data uploads
### Introduction
Given a diff file, we should be able to reverse...
- Put user info in the a/c name in the menu
document created on Mar 14 2022 by Frederick Muriuki Muriithi, last updated on Dec 04 2023 by Frederick Muriuki Muriithi
Put user info in the a/c name in the menu
When the user signs in to GN2, there is no info on the account name in the menu.
## Tags
* assigned: bonfacem
* priority: medium
* status: closed, completed...
- Replace Hard coded authentication with gn-proxy
document created on Mar 14 2022 by Frederick Muriuki Muriithi, last updated on Dec 04 2023 by Frederick Muriuki Muriithi
...Hard coded authentication with gn-proxy
## Tags
* assigned: bonfacem
* priority: medium
* type: enhancement
* status: closed, completed
* keywords: authentication, gn-proxy
## Description
Originally...
- COVID-19
document created on Nov 14 2021 by Pjotr Prins, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
COVID-19
We are setting up a Cloud HPC for COVID-19 using Arvados as the underlying infrastructure.
## Tasks
=> https://github.com/yatisht/usher Fast phylogeny
## Tags
* assigned: pjotrp...
- Adding Terminal Output
document created on Aug 07 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...As GN3 (REST) API handles calling external tools it kinda make sense to handle the terminal output page through GN3 and communicate through websockets. But first I'll do a Sinatra test run.
## Tags...
- Paths in Flask Application
document created on Sep 11 2024 by Frederick Muriuki Muriithi
Paths in Flask Application
## Tags
* type: doc, docs, documentation
* assigned: fredm
* keywords: application paths, flask, absolute path, relative path
## Content
Always build and use absolute paths...
- R/qtl2
document created on Oct 07 2024 by Pjotr Prins
...Tags
* assigned: pjotrp, alexm
* priority: high
* type: enhancement
* status: open
* keywords: database, gemma, reaper, rqtl2
# Description
R/qtl2 handles multi-parent populations, such as DO, HS...
- Shapiro Wilk Test
document created on Nov 24 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...orderNorm function to
perform Ordered Quantile normalization43 on all phenotypes. QTL
--
A quantitative trait variant in Gabra2 underlies increased methamphetamine stimulant sensitivity
```
## Tags...
- Editing Phenotypes
document created on Jul 07 2023 by Frederick Muriuki Muriithi, last updated on Jul 12 2023 by Frederick Muriuki Muriithi
...Tags
* keyword: editing phenotypes
## Introduction
There is old code for editing phenotypes in place, but it was not in use. The main aim at this point is to fix any bugs and adapt it to make use...
- GN-AUTH FAQ
document created on Aug 19 2024 by John Nduli, last updated on Aug 19 2024 by John Nduli
...-AUTH FAQ
## Tags
* type: docs, documentation
* status: ongoing, open
* keywords: authentication, authorisation, docs, documentation
* author: @jnduli
## Quick configuration for local development
Save...
- NGINX Configuration Notes
document created on Jun 01 2023 by Zachary Sloan
NGINX Configuration Notes
## Tags
* type: info, documentation
* keywords: nginx, configurations
## Use of proxy_redirect (in this case for authentication, which runs on GN3 through a GN2 URI)...
- GN3 Error Handling
document created on May 28 2024 by Alexander_Kabui
...Handling
## Tags
* type: docs, documentation
* status: open, ongoing
* keywords: gn3, error_handling, exceptions, docs, documentation
## Introduction
This documentation explains how GN3 handles errors...
- Lisp For Schemers
document created on Dec 29 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...Schemers
## Tags
* type: documentation
* keywords: LISP, Scheme, iota, loop, iterate
## iota
### In Scheme
```
scheme@(guile-user)> (iota 12)
$1 = (0 1 2 3 4 5 6 7 8 9 10 11)
```
### In Common Lisp...
- BNW interface for GN2
document created on Oct 18 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...point.
## Tags
* type: bug
* priority: high
* assigned: pjotrp
* status: in progress
* keywords: BNW
## Todo
The current output reads:
```
<title>Opening BNW</title>
<form method="post" action="http...
- Genotypes, Assemblies, Markers and GeneNetwork
document created on Sep 23 2024 by Frederick Muriuki Muriithi
...Tags
* type: documentation, docs, doc
* keywords: genotype, assembly, markers, data, database, genenetwork, uploader
## Markers
```
The marker is the SNP…
— Rob (Paraphrased)
```
SNPs (Single...
- Types of Data in GeneNetwork
document created on Jul 02 2024 by Frederick Muriuki Muriithi, last updated on Jul 10 2024 by Frederick Muriuki Muriithi
Types of Data in GeneNetwork
## Tags
* assigned:
* priority:
* status: open
* type: documentation
* keywords: gn-uploader, uploader, genenetwork, documentation, doc, docs, data, data type, types...
- Adding Platforms
document created on Apr 04 2024 by Frederick Muriuki Muriithi, last updated on Apr 24 2024 by Frederick Muriuki Muriithi
Adding Platforms
## Tags
* status: open
* priority: medium
* type: documentation
* assigned: fredm, flisso, acenteno
* keywords: doc, documentation, platform, gn-uploader, uploader, adding data...
- Weechat
document created on Nov 04 2021 by Pjotr Prins, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...Tags
* type: documentation
* keywords: cli, weechat, documentation
Weechat is a very versatile terminal chat that can handle IRC, Matrix and Slack.
## Weechat install + slack
Arun has packaged...
- MariaDB
document created on Oct 26 2021 by Pjotr Prins, last updated on Feb 20 2024 by Pjotr Prins
...below and
=> topics/deploy/installation
# Tags
* type: info, documentation
* keywords: mariadb, systems
# Check the transaction logs
Start the client and:
```
MariaDB [db_webqtl]> show binary logs...
- Improving Metadata Audit
document created on Jul 25 2023 by Frederick Muriuki Muriithi, last updated on Aug 11 2023 by Frederick Muriuki Muriithi
...Tags
* assigned: fredm
* priority: high
* keywords: editing, metadata, metadata audit
* type: documentation
* status: open
## Introduction
There is an existing metadata audit system that tracks...
- Fallbacks
document created on Feb 18 2024 by Pjotr Prins, last updated on Apr 09 2024 by Pjotr Prins
...fallback servers using Arun's Guix machine configuration. Outside the system container there are a few dependencies, particularly MariaDB and a number of file directories.
# Tags
* assigned: pjotrp...
- Implementation of QTL Analysis Using r-qtl2 in GeneNetwork
document created on Nov 12 2024 by Alexander_Kabui, last updated on Nov 12 2024 by Alexander_Kabui
...Tags
* Assigned: alexm
* Keywords: RQTL, GeneNetwork2, implementation
* Type: Feature
* Status: In Progress
## Description
This document outlines the implementation of a QTL analysis tool...
- BigBlueButton
document created on Mar 05 2022 by jgart, last updated on Feb 28 2023 by Pjotr Prins
...Tags
* type: documentation
* keywords: BigBlueButton
## BASH script to install BigBlueButton in 30 minutes.
https://github.com/bigbluebutton/bbb-install
```
wget -qO- https://ubuntu.bigbluebutton...
- Top 10 Things to Test
document created on Mar 28 2022 by BonfaceKilz
...10 Things to Test
## Tags
* assigned: bonfacem
* type: tests
* keywords: documentation, testing, checklist
## Introduction
Important things:
- Correctness
- Speed (fast enough)
- Reliability
Let's do...
- GN Services
document created on Sep 15 2021 by Pjotr Prins, last updated on Dec 23 2022 by Pjotr Prins
...Tags
* type: documentation
* status: in progress
* keywords: gn services, documentation
# Description
First make sure to have a stable guix checkout. E.g.
```
gn3@tux01:~/production/gn-proxy$ /home/...
- Shepherd
document created on Aug 27 2021 by Pjotr Prins, last updated on Dec 02 2023 by Pjotr Prins
Shepherd
Here we record information on running shepherd (on Debian).
# Tags
* assigned: pjotrp, efraimf
* type: documentation
* keywords: system, shepherd
* status: wip
* priority: normal...
- Adding Species
document created on Apr 24 2024 by Frederick Muriuki Muriithi, last updated on Apr 24 2024 by Frederick Muriuki Muriithi
Adding Species
## Tags
* status: open
* priority: medium
* type: documentation
* assigned: fredm, flisso, acenteno
* keywords: doc, documentation, platform, gn-uploader, uploader, adding data...
- Add Metadata To The Trait Page (RDF)
document created on Sep 28 2022 by Munyoki Kilyungi, last updated on Dec 03 2023 by Pjotr Prins
...and contributors.
* Add metadata as links, tooltips, or html <summary> tag to the relevant html section(s).
## Resources
=> https://www.linkedin.com/pulse/six-secret-sparql-ninja-tricks-kurt-cagle/
- Mechanical Rob
document created on Aug 23 2022 by Arun Isaac, last updated on Aug 16 2024 by Munyoki Kilyungi
...Tags
* type: documentation, docs
* assigned: bonfacem, rookie101, fredm
* priority: medium
* status: open
* keywords: tests, testing, mechanical-rob
## What is Mechanical Rob?
Mechanical Rob is our...
- Invoking SQLite3: CLI
document created on Mar 30 2024 by Frederick Muriuki Muriithi
...Tags
* status:
* assigned:
* priority:
* type: documentation
* keywords: doc, documentation, sqlite, sqlite3
## TLDR
At minimum, always invoke sqlite with "PRAGMA foreign_keys = ON;" as follows...
- Phenotype Naming Conventions
document created on Nov 23 2022 by Munyoki Kilyungi, last updated on Dec 03 2023 by Pjotr Prins
...BW_M_6m* as the body weight of males at 6 months for 6 or more publications. Then we may need to programmatically add further tags such as year of publication (last two digits).
3. We have to decide...
- Generating Key-Pairs
document created on Apr 18 2024 by Frederick Muriuki Muriithi, last updated on Apr 22 2024 by Frederick Muriuki Muriithi
...Key-Pairs
## Tags
* type: documentation
* keywords: doc, documentation, gn-auth, key-pair, jwt
## Generating the Key-Pair
If openssl is not present on your system, you need to get it. You can either...
- GeneNetwork Services
document created on Oct 26 2024 by Frederick Muriuki Muriithi, last updated on Nov 01 2024 by Frederick Muriuki Muriithi
...Tags
* type: documentation
* keywords: documentation, docs, doc, services, genenetwork services
## GeneNetwork Core Services
GeneNetwork is composed of a number of different services. This document...
- Common Lisp Condition Handling
document created on Dec 28 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
.../Condition-Handling-2001.html Condition Handling in the Lisp Language Family
=> https://gigamonkeys.com/book/beyond-exception-handling-conditions-and-restarts.html Conditions and Restarts
## Tags...
- Fire up system container for GN-QA System
document created on May 13 2024 by Munyoki Kilyungi, last updated on May 13 2024 by Munyoki Kilyungi
Fire up system container for GN-QA System
# Tags
* assigned: bonfacem, alexm
The current code is a WIP. Patches will be sent after a working container is set-up. Most recent code can be found at...
- Deploying Your Flask Application Under a URL Prefix With GUnicorn
document created on Oct 17 2024 by Frederick Muriuki Muriithi
Deploying Your Flask Application Under a URL Prefix With GUnicorn
## TAGS
* type: doc, documentation, docs
* author: fredm, zachs
* keywords: flask, gunicorn, SCRIPT_NAME, URL prefix
## Introduction...
- How to upgrade slurm on octopus
document created on Aug 29 2024 by Arun Isaac, last updated on Oct 18 2024 by Arun Isaac
...it is safe to upgrade version 18.08 to 19.05 or 20.02, but not to 20.11 or later. This compatibility information is in the RELEASE_NOTES file of the slurm git repo with the git tag corresponding...
- Data Uploads: Inserting Data
document created on Jan 27 2022 by BonfaceKilz, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...Tags
* assigned: bonfacem, zachs
* type: bug
* priority: high
* status: in progress
* keywords: data uploads
### Introduction
The current uploader work documented in `editing-data.gmi` only caters...
- Logging with Flask and Gunicorn
document created on Apr 15 2024 by Frederick Muriuki Muriithi
...Tags
* type: documentation
* keywords: deploy, deployment, logging, flask, gunicorn
## Logging with Flask and Gunicorn
Flask has its own output logger, `flask.logger`, which is an extension...
- Editing Case-Attributes
document created on Jul 07 2023 by Frederick Muriuki Muriithi, last updated on Sep 09 2024 by Munyoki Kilyungi
...Tags
* type: document
* keywords: case-attribute, editing
* assigned: fredm, zachs, acenteno, bonfacem
* status: requirements gathering
## Introduction
Case-attributes metadata for samples. They...
- Using PDB to Troubleshoot Python Code
document created on Dec 03 2023 by Pjotr Prins
...Code
## Tags
* type: documentation
* keywords: debugging, python
Historically, debugging GeneNetwork code has been a bit of a pain where you would have `print' and `logging' statements to help view...
- GeneNetwork Authentication/Authorisation Architecture
document created on Dec 04 2023 by Frederick Muriuki Muriithi, last updated on Jul 25 2024 by Frederick Muriuki Muriithi
.../Authorisation Architecture
## Tags
* type: docs, documentation
* status: ongoing, open
* keywords: authentication, authorisation, architecture, docs, documentation
* author: Frederick Muriuki Muriithi...
- Partial Correlation
document created on Oct 15 2021 by Frederick Muriuki Muriithi, last updated on May 16 2022 by Frederick Muriuki Muriithi
...Add in search results.
Pick 3 and hit 'Partial'
Put one each in X, Y and Z columns
And compute against database (lower half).
That gives you a list of hits.
## Members
* fredm
* pjotp
* alex
## Tags...
- Data Upload Process
document created on Apr 30 2024 by Munyoki Kilyungi, last updated on Apr 30 2024 by Munyoki Kilyungi
...Upload Process
## Tags
* assigned: priscilla
* keywords: documentation, gn-uploader
The process of uploading data to the GeneNetwork platform began with retrieving the dataset from the Gene Network...
- GeneNetwork Hacking Documentation
document created on Mar 11 2022 by Frederick Muriuki Muriithi, last updated on Jul 18 2022 by Frederick Muriuki Muriithi
...to help with clarifying some concepts and critiquing the documentation.
The goal of this document is to encourage and track the documentation that assist with the development of the system.
## Tags...
- Precompute steps
document created on May 07 2024 by Pjotr Prins, last updated on Aug 16 2024 by Pjotr Prins
...Compute bulklmm vector
Interestingly this work coincides with Arun's work on CWL. Rather than trying to write a workflow in bash, we'll use ccwl and accompanying tools to scale up the effort.
# Tags...
- Automated Testing
document created on Oct 12 2022 by Munyoki Kilyungi, last updated on Dec 03 2023 by Pjotr Prins
...Testing
## Tags
* keywords: testing, CI, CD
## Introduction
As part of the
=> ../systems/ci-cd.gmi CI/CD effort
there is need for automated tests to ensure that the system is working as expected.
- Borg backups
document created 2 days ago by Pjotr Prins, last updated 25 hours ago by Pjotr Prins
...essentially wraps a Unix command and sends a report to a local or remote redis instance.
Sheepdog also includes a web server for output:
=> http://sheepdog.genenetwork.org/sheepdog/status.html
# Tags...
- Fire up system container for GN
document created on Mar 02 2024 by Pjotr Prins, last updated on Apr 05 2024 by Pjotr Prins
Fire up system container for GN
# Tags
* assigned: pjotrp
* priority: medium
* type: system administration
* keywords: system administration, GN, tux01, tux02, tux04, balg01
# Tasks
We have the...
- Editing Data
document created on Nov 23 2021 by BonfaceKilz, last updated on Jul 25 2023 by Frederick Muriuki Muriithi
...Tags
* assigned: bonfacem
* keywords: metadata
* status: unclear
* priority: medium
### Introduction
At the moment, you can edit metadata related to a published phenotype and a probeset. When an...
- Deploying gn-auth
document created on Mar 04 2024 by Frederick Muriuki Muriithi, last updated on Mar 12 2024 by Frederick Muriuki Muriithi
Deploying gn-auth
## Tags
* type: doc, docs, documentation
* keywords: gn-auth, deployment
* status:
* priority:
* assigned:
## …
︙
### Run Migrations
At this point, you have a container running...
- Configuring Nginx on the Host System
document created on Aug 27 2024 by Frederick Muriuki Muriithi
Configuring Nginx on the Host System
## Tags
* type: doc, docs, documentation
* keywords: deploy, deployment, deploying, nginx, guix, guix container, guix system container
* status: in progress...
- RQTL Implementation for GeneNetwork Design Proposal
document created on Oct 15 2024 by Alexander_Kabui, last updated on Nov 12 2024 by Alexander_Kabui
...Design Proposal
## Tags
* Assigned: alexm,
* Keywords: RQTL, GeneNetwork2, Design
* Type: Enhancements,
* Status: In Progress
## Description
This document outlines the design proposal for the re-...
- Binding notebooks
document created on Aug 22 2021 by jgart, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...R/shiny notebooks and Pluto notebooks. These binding tools do a lot more and do not leverage GNU Guix lightweight container infrastructure. In this project we want to create a binding-lite.
## Tags...
- GeneNetwork Uploader Requirements
document created on Feb 22 2024 by Frederick Muriuki Muriithi, last updated on Feb 22 2024 by Frederick Muriuki Muriithi
...Uploader Requirements
*OR*: "Reattaching the Head on Frederick's Headless-Chicken Development :-)"
## Tags
* assigned: fredm, flisso
* type: doc, requirements
* priority: high
* status: open...
- Migrate GN1 Clustering
document created on Jul 18 2021 by Pjotr Prins, last updated on Mar 22 2022 by Frederick Muriuki Muriithi
...map' icons. Computation may take a while.
Next click on 'Cluster traits' and 'Redraw' map. This is the one we want in GN3/GN2!
=> ./heatmap.png
## Members
* fredm
* pjotr
## Kanban
* fredm
## Tags...
- MariaDB Database Architecture
document created on Jun 29 2024 by Pjotr Prins, last updated on Sep 02 2024 by Lisso_
...measured mRNA level, and the vendor called their assays "ProbeSets". We used this now obsolete term. Most ProbeSetData in GN1 and GN2 as of 2024 are measurments of molecular traits that can be tagged...
- Meeting Notes
document created on Jun 11 2024 by John Nduli, last updated 5 weeks ago by Munyoki Kilyungi
...tag for paper1: Fix this with Boni and get done later on/iron them out then.
* @bmunyoki fix CI job that transforms gn tables to TTL: Move this to running a cron job once per month instead of
## 2024-...
- Precompute mapping input data
document created on Mar 20 2023 by Pjotr Prins, last updated on Jun 03 2024 by Pjotr Prins
...updated traitid, i.e., DataId from ProbeSetXRef which is indexed. Before doing anything we use Locus_old to identify updates by setting it to NULL. See the header of list-traits-to-compute.scm.
# Tags...