indel-mapper
GPL-3.0 License
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Indel Mapper
Set up
First, make sure the correct version of virtualenv is installed:
$ pip3 install virtualenv
Next, cd into your project and set up the virtualenv directory:
$ virtualenv --python=python3 indel-mapper
Activate virtualenv. This adds the indel-mapper/bin directory to the start
of your $PATH.
$ source indel-mapper/bin/activate
Install the required libraries:
$ pip3 install -r requirements.txt
Install the Redis server. The instructions for this will vary depending on your operating system. For Debian, Ubuntu, and derivatives,
$ sudo apt install redis-server
Starting the Web application
Run the application:
$ python3 app.py
Start Redis. How you do this depends on your operating system.
Debian, Ubuntu, or derivatives:
$ sudo systemctl start redis-server
Run Celery
$ indel-mapper/bin/celery worker -A app.celery --loglevel=info
Running the test suite
Run the tests:
$ python3 -m unittest
Deploying to Heroku
$ git push heroku master
Running locally as a command line application
Example:
$ python3 run.py -a ~/Documents/bowtie2_results.sam -r ~/Documents/references.csv -o ~/Documents/results.csv
There are three required arguments:
-
-aor--alignmentAlignment SAM file -
-ror--referenceReference CSV file -
-oor--outputOutput file, in CSV
License
Indel Mapper is licensed under Version 3 of the GNU General Public License.
Badges
Extracted from project README
