Package: chanjo-report
Chanjo ReportAutomatically generate basic coverage reports from Chanjo SQL databases. This plugin installs as a subcommand ("report") to the Chanjo command line interface.UsageChanjo Report supports a number of output formats: tabular, PDF, and HTML. To print a PDF coverage report for a group of samples "WGS-prep" do:$chanjoreport--renderpdf--group"WGS-prep">./coverage-report.pdfFeaturesSupported output formatsChanjo Reports multiple output formats:tabular: easily parsable and pipeablePDF: easily distributable (for humans)HTML: easily deliverable on the webSupported languages (translations)The coverage report (HTML/PDF) can be render is the following languages:EnglishSwedishMotivationWe are using the output from Chanjo at Clincal Genomics to report success of sequencing across the exome based on coverage. Our customers, clinicians mostly, are specifically interested in knowing to what degree their genes of interest are covered by sequencing along with some intuitive overall coverage metrics. They want the output in PDF format to file it in their system.As a side effect of finding it easiest to convert HTML to PDF, Chanjo Report has a built in Flask server that can be used to render reports dynamically and even be plugged into other Flask servers as a Blueprint.InstallationThe latest version of Chanjo-report can be installed by cloning and installing the repository from Clinical Genomics github:$gitclonehttps://github.com/Clinical-Genomics/chanjo-report.git
$cdchanjo-report
$pipinstall--editable.Demo instance with DockerTo run a local demo with Docker, ensure you have a Docker engine running.
If you do not have Docker set up, we can recommend Docker Desktop (https://www.docker.com/products/docker-desktop/).Then usemakewith the repositoryMakefileto build and run:makebuild
makesetup
makereportPoint your browser tohttp://127.0.0.1:5000and find the demo samples.Comprehensive instructionsWe provide a Dockerfile to run the server in a container. To run a demo instance of the server with a pre-populated database consisting of a case with 3 samples, clone the repository using the following commands:$gitclonehttps://github.com/Clinical-Genomics/chanjo-report.git
$cdchanjo-reportThen you could make use of the services present in the Docker-compose file following these 3 steps:Build the imagesmakebuildLaunch chanjo to create a populate the database with demo datamakesetupLaunch the chanjo-report servermakereportA running instance of the server should now be available at the following url:http://localhost:5000/.In order to generate a report containing all 3 demo samples, use the respective request args:http://localhost:5000/report?sample_id=sample1&sample_id=sample2&sample_id=sample3Please be aware that if you are building and running the Dockerized version of chanjo-report, there might beissues onmacOSif your processor is Apple silicon(or anotherARM64based architecture).
In order to build thechanjo-reportimage in theARM64architecture, you can set the environment variableDOCKER_DEFAULT_PLATFORM:exportDOCKER_DEFAULT_PLATFORM=linux/amd64
makebuild
makesetup
makereportLicenseMIT. See theLICENSEfile for more details.ContributingAnyone can help make this project better - readCONTRIBUTINGto get started!