Releases: bioinfodlsu/rice-pilaf
v1.0.9
Welcome! RicePilaf is short for Rice Post-GWAS/QTL Analysis dashboard. Ok, so we are not great at acronyms; but like a flavorful rice pilaf that combines many ingredients, this RicePilaf combines information from multiple rice databases to provide insights into your QTL/GWAS loci.
Installation and Usage
Please visit the wiki.
Changelog
- No changes to the source code compared to v1.0.8. This version is merely for testing whether Watchtower is properly configured to update the deployed container on the Bioinformatics Lab's server upon the release of a new image.
v1.0.8
Welcome! RicePilaf is short for Rice Post-GWAS/QTL Analysis dashboard. Ok, so we are not great at acronyms; but like a flavorful rice pilaf that combines many ingredients, this RicePilaf combines information from multiple rice databases to provide insights into your QTL/GWAS loci.
Installation and Usage
Please visit the wiki.
Changelog
-
Implemented workflow to automatically update the deployment on the Bioinformatics Lab's server every time a new version is released. This change includes the addition of a new image in the GitHub Container registry (
deploy-bioinfodlsu) and custom nginx configuration files.Refer to this section of our wiki for the updated instructions on deploying RicePilaf to our lab's server.
v1.0.7
Welcome! RicePilaf is short for Rice Post-GWAS/QTL Analysis dashboard. Ok, so we are not great at acronyms; but like a flavorful rice pilaf that combines many ingredients, this RicePilaf combines information from multiple rice databases to provide insights into your QTL/GWAS loci.
Installation and Usage
Please visit the wiki.
Changelog
- No changes to the source code compared to v1.0.6. This version is merely for testing whether Watchtower is properly configured to update the deployed container upon the release of a new image.
v1.0.6
Welcome! RicePilaf is short for Rice Post-GWAS/QTL Analysis dashboard. Ok, so we are not great at acronyms; but like a flavorful rice pilaf that combines many ingredients, this RicePilaf combines information from multiple rice databases to provide insights into your QTL/GWAS loci.
Installation and Usage
Please visit the wiki.
Changelog
- Revised note on top of the deployed website. The note now reads: "For heavy workloads, consider running RicePilaf locally. Click here to install"
v1.0.5
Welcome! RicePilaf is short for Rice Post-GWAS/QTL Analysis dashboard. Ok, so we are not great at acronyms; but like a flavorful rice pilaf that combines many ingredients, this RicePilaf combines information from multiple rice databases to provide insights into your QTL/GWAS loci.
Installation and Usage
Please visit the wiki.
Changelog
- No changes to the source code compared to v1.0.4. This version is merely for testing whether Watchtower is properly configured to update the deployed container upon the release of a new image.
v1.0.4
Welcome! RicePilaf is short for Rice Post-GWAS/QTL Analysis dashboard. Ok, so we are not great at acronyms; but like a flavorful rice pilaf that combines many ingredients, this RicePilaf combines information from multiple rice databases to provide insights into your QTL/GWAS loci.
Installation and Usage
Please visit the wiki.
Changelog
- Modified the GitHub Actions workflow to tag the latest versions of the Docker images as
latest. Doing so allows the deployed container to be automatically updated using tools like Watchtower once a new version is released. - Wrote a shell script for commands that have to be run inside the container after an update. Running this shell script can be automated using Watchtower's lifecycle hooks. Previously, a sysadmin would have to manually run
docker execto execute these commands.
v1.0.3
Welcome! RicePilaf is short for Rice Post-GWAS/QTL Analysis dashboard. Ok, so we are not great at acronyms; but like a flavorful rice pilaf that combines many ingredients, this RicePilaf combines information from multiple rice databases to provide insights into your QTL/GWAS loci.
Installation and Usage
Please visit the wiki.
Changelog
- Improved the handling of invalid genomic interval inputs, along with the user-facing error messages
- Fixed the display of the warning message when invalid accessions are entered in the "additional genes" box (on the coexpression and regulatory feature enrichment pages). The warning message is now persistently displayed even after the results are loaded, and it is cleared when the user clicks "Reset All Analyses."
- Minor front-end edits
v1.0.2
Welcome! RicePilaf is short for Rice Post-GWAS/QTL Analysis dashboard. Ok, so we are not great at acronyms; but like a flavorful rice pilaf that combines many ingredients, this RicePilaf combines information from multiple rice databases to provide insights into your QTL/GWAS loci.
Installation and Usage
Please visit the wiki.
Changelog
-
Rewrote the (data preparation) workflow Dockerfile. Previously, R 4.3 and Bioconductor 3.17 were installed on top of the
python:3.10-bullseyebase image. For reproducibility, it is imperative to use these versions of R and Bioconductor. However, the most recent version of Bioconductor (3.19) requires R 4.4, while attempting to install Bioconductor 3.17 packages from source leads to dependency issues.As a solution, we rewrote the Dockerfile to use the
bioconductor/bioconductor_docker:RELEASE_3_17-R-4.3.0base image instead. Aside from simplifying the installation of R packages, this change also reduced the image building time from ~24 minutes to ~8 minutes. -
Simplified the logic for deciding on whether to fetch the Bootstrap and Font Awesome stylesheets and sprites via the jsDelivr CDN or to use the self-hosted versions
-
Added more code documentation, as well as GitHub Actions workflow documentation
v1.0.1
Welcome! RicePilaf is short for Rice Post-GWAS/QTL Analysis dashboard. Ok, so we are not great at acronyms; but like a flavorful rice pilaf that combines many ingredients, this RicePilaf combines information from multiple rice databases to provide insights into your QTL/GWAS loci.
Installation and Usage
Please visit the wiki.
Changelog
- Replaced
import *with explicit imports to avoid namespace pollution - Revised CI/CD workflow for isort to enforce compatibility with Black formatting
v1.0.0
Welcome! RicePilaf is short for Rice Post-GWAS/QTL Analysis dashboard. Ok, so we are not great at acronyms; but like a flavorful rice pilaf that combines many ingredients, this RicePilaf combines information from multiple rice databases to provide insights into your QTL/GWAS loci.
Installation and Usage
Please visit the wiki.
Changelog
- Updated the app (i.e., the version intended for local installation) so that its front-end styling is retained even when run offline
- Implemented cron jobs for (i) sending app usage logs to us and (ii) clearing the directory where results of previously run analyses are cached to prevent repeated computations. Note that these cron jobs are triggered only in the version of the app intended for deployment. Moreover, sending app usage logs is entirely optional and requires express consent from the organization deploying RicePilaf and an authorized service key from us. The logs will be used only to help us improve RicePilaf. More details here.
- Added a CI/CD workflow for checking if the Python imports in the codebase are sorted as per the convention followed by the
isortutility - Edited the Dockerfile for the workflow to explicitly install R 4.3. Previously, it installed the latest stable version of R in Debian "bullseye"