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Website to analyze conflicting assertions in ClinVar
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static
templates
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Makefile
README.md
asynchelper.py
clinvar-miner.py
clinvar-miner.wsgi
create-indexes.py
db.py
get-submitter-info.py
import-all-clinvar-xmls.sh
import-clinvar-xml.py
import-latest-clinvar-xml.sh
mondo.py
nonstandard_significance_terms.tsv
requirements.txt
start-dev.sh
submitter_info.tsv

README.md

Getting started

  1. Install Make, cURL, Python 3, and Pip 3 from your system package manager.

  2. Run pip3 install -r requirements.txt to install required Python packages.

  3. Run make countries to update information about ClinVar submitters and their countries.

  4. Check submitter_info.tsv to make sure that that the country information is complete and correct (git diff is an easy way to look). Make any needed changes.

  5. Run make to build the ClinVar Miner database. This process takes about 24 hours. If you wish to omit historical ClinVar data, run make latest instead, which takes about 1 hour.

  6. For development, run ./start-dev.sh and open http://localhost:5000/ in your web browser. You can change the port number by passing -p <port>.

    For production, point your web server to clinvar-miner.wsgi. For example, if you are using Apache, the configuration would look like:

    Timeout 300
    WSGIDaemonProcess wsgi
    WSGIProcessGroup wsgi
    WSGIScriptAlias /clinvar-miner /var/www/clinvar-miner/clinvar-miner.wsgi
    WSGIApplicationGroup %{GLOBAL}
    LimitRequestLine 1000000
    LimitRequestFieldSize 1000000
    
  7. To update ClinVar Miner after each month's ClinVar release, repeat steps 3 and 4 and then run make latest.

License

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

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