sudo
to run docker
and docker-compose
. Otherwise you will have issues running this demo. Check docker run hello-world
runs without problem. If you have permissions issues, see how to run docker as-non-root user.git submodule
folders isabl_api
and isabl_cli
are not empty. If they are, probably the --recurse-submodules
flag didn't work. git submodule update --recursive
--initdemo-compose down
to stop the application.demo-django createsuperuser
to create one!demo-compose
, demo-django
, and demo-cli
are simple wrappers around docker-compose
- check them out. The isabl_demo
directory was bootstrapped using cookiecutter-isabl, a proud fork of cookiecutter-django! Many topics from their guide will be relevant to your project.isabl-cli
know where can the API be reached, and what CLI settings we should use (if you are using demo-compose
, these variables are already set):isabl-cli
:isabl-cli
to add choices for Center, Disease, Sequencing Technique, and Data Generating Platform:demo_submission.xlsm
file into the submit samples form:fx
documentation. Use --help
to learn about other ways to visualize metadata (e.g. tsv
).isabl-cli
will move our test data, let's copy original assets into a staging directory:--data-id
flag, the command get-reference
also allows you to retrieve the indexes generated during import. To get a list of available files per assembly run:--commit
to complete the operation.--commit
to deploy):--force
.2:123,028-123,995
in the locus bar, that's were our test data has reads. Learn more about default BAMs in the Writing Applications guide.qc-data
application are available at an experiment, individual, and project level. In this example we are looking at the project-level auto-merge analysis:get-paths
:ipython
: