SSEC-JHU SnapMine

About

Web application for junction or gene expression count extraction and analysis:

• Preprint at: Large-scale RNA-seq mining reveals ciclopirox triggers TDP-43 cryptic exons
• SnapMine is deployed at: https://snapmine.idies.jhu.edu/

Initial Setup:

• Get the code: git clone https://github.com/ssec-jhu/snaptron-query.git
• Then you will need to download the metadata files for the dataset of interest (or all) in a folder, renaming each file with the dataset name as prefix:
  • srav3h to srav3h_samples.tsv
  • gtexv2 to gtexv2_samples.tsv
  • tcgav2 to tcgav2_samples.tsv
  • srav1m to srav1m_samples.tsv
  • encode to encode1159_samples.tsv
  • Change the meta_data_directory string in snaptron-query/snaptron_query/app/paths.py to the directory of the metadata files downloaded

Build & Run:

Follow above setup instructions if you have not done so already.

with Tox [running locally]:

• pip install tox if you don't have it already
• Make sure you are in the repo directory: cd snaptron-query
• You should see the tox file: tox.ini
• Run: tox -e test exec -- python -m snaptron_query.app.main_dash_app
• This will have Dash running locally on http://127.0.0.1:8050/
• Ctrl+c to quit

with Python ecosystem [running locally]:

• Make sure you are in the repo directory: cd snaptron-query
• Run python3 -m snaptron_query.app.main_dash_app
• This will have Dash running locally on http://127.0.0.1:8050/
• Ctrl+c to quit

Using tox to run tests

• Run tox tox. This will run all of linting, security, test, docs and package building within tox virtual environments.
• To run an individual step, use tox -e {step} for example:
  • tox -e format
  • tox -e test
  • tox -e build-docs
  • tox -e format

Typically, the CI tests run in github actions will use tox to run as above. See also ci.yml.