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 exec to 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-bullseye base 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-4.3.0 base 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 isort utility
• Edited the Dockerfile for the workflow to explicitly install R 4.3. Previously, it installed the latest stable version of R in Debian "bullseye"

v0.1.4

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

• Refactored the logic for retrieving the version number and for checking whether the app is for deployment or local installation. Previously, these are specified in separate files (.version and .deploy). These settings are now bundled in a single .env file
• Modified the Dockerfile to include the generation of this .env file
• Disabled debugging mode in the version of the app intended for local installation. Debugging mode is now switched on only for development purposes
• Minor updates to the README and the column header tooltips in the summary page

v0.1.3

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

• Overrode the default nginx.conf in order to increase the timeout window to 5 minutes. This allows the execution of long-running processes, such as regulatory feature enrichment
• Enforced code formatting using Black instead of autopep8. Checking for compliance with Black formatting is also now integrated into the CI/CD pipeline
• Revised CI/CD workflows to ensure that dependent workflows are executed only when preceding workflows completed successfully (previously, only completion, regardless of result, was checked)
• Added more code documentation

v0.1.2

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

• Added the version release number to the app's footer. The release number is read from a file named .version, which is automatically included when using the image we published in the GitHub Container registry
• Changed the base image of our workflow image to python3:10-bullseye. Previously, it was tiangolo/uwsgi-nginx-flask:python3.10; however, uwsgi and nginx are technically not needed for data preparation. This change also reduces the size of the image
• Revised workflow for publishing a release. The release branch is now pushed to the main branch before publishing a release
• Added more files to .gitignore and .dockerignore
• Added list of publicly accessible running instances (RicePilaf URLs) to our README

v0.1.1

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

• Enforced distinction between locally installed version and deployed version. For example, a locally installed version should display the "Clear Cache" button, while the deployed version should not display it
• Edited the Dockerfile for the locally installed version (app) so as to not use uwsgi and nginx and instead just use Flask's built-in server. This resulted in a ~360 MB decrease in the size of the image
• Created a separate Dockerfile for the deployed version (deploy), which uses uwsgi and nginx. Previously, this was the Dockerfile for the locally installed version (app), with the addition of an extra command for specifying that the app should run in deployed mode
• Incorporated the Dockerization of the deployed version into the GitHub Actions workflow. There are now three images in the GitHub Container Registry (app, workflow, and deploy)
• Updated CONTRIBUTING.md to include information on raising issues, contributing to the codebase, license, code of covenant, and contact