| Age | Commit message (Expand) | Author |
|---|
| 2022-03-12 | README: Replace "unit-test" instructions with "pytest" | BonfaceKilz |
| 2022-03-04 | Document basic partial correlations dependencies...* Document the things that the partial correlations feature depends on to work
| Frederick Muriuki Muriithi |
| 2022-02-02 | Revert "Use guix shell shortcut with guix.scm file"...This reverts commit f676c291967f8a81836b73c5a5dcd3c65e02552c.
| BonfaceKilz |
| 2022-01-27 | Use guix shell shortcut with guix.scm file | jgart |
| 2022-01-24 | README: Add pylint and mypy CI badges....We now have separate CI jobs for the pylint and mypy tests.
* README.md: Add pylint and mypy CI badges.
| Arun Isaac |
| 2022-01-21 | README: Update link to CI badge....The CI has been moved to penguin2, and this is accompanied by a URI change.
* README.md: Update link to CI badge.
| Arun Isaac |
| 2022-01-01 | guix_deploy | Pjotr Prins |
| 2021-12-09 | README: Link CI badge to CI status page....* README.md: Link CI badge to CI status page.
| Arun Isaac |
| 2021-12-09 | README: Add CI badge....* README.md: Add CI badge.
| Arun Isaac |
| 2021-11-19 | Replace guix environment with guix shell....* README.md, guix.scm: Replace guix environment with guix shell.
| Arun Isaac |
| 2021-11-11 | Disuse absolute paths to guix....It is safe to assume that the user has correctly set up guix in their PATH.
* README.md: Disuse absolute paths to guix in command invocations.
| Arun Isaac |
| 2021-11-11 | Disuse GUIX_PACKAGE_PATH....guix-bioinformatics is a Guix channel that is set up by `guix pull'. There is
no need to specify it explicitly using GUIX_PACKAGE_PATH.
* README.md: Do not explicitly set GUIX_PACKAGE_PATH for any command.
| Arun Isaac |
| 2021-08-31 | Merge branch 'main' of github.com:genenetwork/genenetwork3 into heatmap_gener... | Muriithi Frederick Muriuki |
| 2021-08-30 | Update documentation on genotype files...* Provide documentation on downloading and using the genotype files.
| Muriithi Frederick Muriuki |
| 2021-08-30 | Fix issues with traits file format...* README.md: update header: Traits ==> Trait
* gn3/computations/qtlreaper.py: update header: Traits ==> Trait
* qtlfilesexport.py: Choose only BXD strains
Rename the first column header from "Traits" to "Trait" to correspond with
what `rust-qtlreaper` expects.
Choose only the BXD strains for the proof-of-concept example - this helped
bring out the fact that the traits file SHOULD NOT contain a strain column
for a strain that does not exist in the genotype file in consideration.
If the traits file has a strain column which does not exist in the genotype
file, then `rust-qtlreaper` fails with a panic, since, from what I can tell,
it tries to get a value from the genotype file for the non-existent strain,
which results to a `None` type. Subsequent attempts at running an operation
on the `None` type lead to the panic.
| Muriithi Frederick Muriuki |
| 2021-08-30 | Document acquired knowledge on `rust-qtlreaper`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/heatmaps/heatmaps.py: document format of the traits file
To assist future developers, and development of the system, this commit
documents some of the hard-won knowledge about the operation of the system
to ease future development of the system.
The documentation, if good, might also help with future onboarding of new
developers to the system.
| Muriithi Frederick Muriuki |
| 2021-08-28 | README: updated install instructions | Pjotr Prins |
| 2021-08-28 | Add explanation of using a guix profile | Pjotr Prins |
| 2021-08-07 | Add gunicorn support for production | Pjotr Prins |
| 2021-08-07 | Update info on running guix container | Pjotr Prins |
| 2021-05-14 | README | Pjotr Prins |
| 2021-03-17 | README: Update instructions on how to freeze packages | BonfaceKilz |
| 2021-03-17 | README: Add extra note on deps | BonfaceKilz |
| 2021-03-17 | README: Add note on how to force install things in venv | BonfaceKilz |
| 2021-02-17 | Add gemma-wrapper...* guix.scm: New package propagated-input.
* README.md: Mention that you require "guix-bioinformatics" package, because
of the addition of "gemma-wrapper".
| BonfaceKilz |
| 2021-02-16 | Add instructions on how to run the flask app | BonfaceKilz |
| 2021-02-15 | Update README with bootstrap instructions and how to run tests | BonfaceKilz |
| 2021-02-11 | Initial commit | Pjotr Prins |
