GPL-3.0 License
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
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
Run the tests:
$ python3 -m unittest
$ git push heroku master
Example:
$ python3 run.py -a ~/Documents/bowtie2_results.sam -r ~/Documents/references.csv -o ~/Documents/results.csv
There are three required arguments:
-a
or --alignment
Alignment SAM file-r
or --reference
Reference CSV file-o
or --output
Output file, in CSVIndel Mapper is licensed under Version 3 of the GNU General Public License.