https://github.com/hrs/indel-mapper
https://github.com/hrs/indel-mapper
biology flask python
Last synced: 5 months ago
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- Host: GitHub
- URL: https://github.com/hrs/indel-mapper
- Owner: hrs
- License: gpl-3.0
- Created: 2017-03-18T17:40:08.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2017-07-23T20:47:26.000Z (almost 9 years ago)
- Last Synced: 2025-04-04T17:07:07.265Z (about 1 year ago)
- Topics: biology, flask, python
- Language: Python
- Homepage: http://indel-mapper.herokuapp.com/
- Size: 178 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 9
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
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README
# Indel Mapper
[](http://www.gnu.org/licenses/gpl-3.0)
## Set up
First, make sure the correct version of `virtualenv` is installed:
```shell
$ pip3 install virtualenv
```
Next, `cd` into your project and set up the `virtualenv` directory:
```shell
$ virtualenv --python=python3 indel-mapper
```
Activate `virtualenv`. This adds the `indel-mapper/bin` directory to the start
of your `$PATH`.
```shell
$ source indel-mapper/bin/activate
```
Install the required libraries:
```shell
$ 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,
```shell
$ sudo apt install redis-server
```
## Starting the Web application
Run the application:
```shell
$ python3 app.py
```
Start Redis. How you do this depends on your operating system.
**Debian, Ubuntu, or derivatives:**
```shell
$ sudo systemctl start redis-server
```
Run Celery
```shell
$ indel-mapper/bin/celery worker -A app.celery --loglevel=info
```
## Running the test suite
Run the tests:
```shell
$ python3 -m unittest
```
## Deploying to Heroku
```shell
$ git push heroku master
```
## Running locally as a command line application
Example:
```shell
$ 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 CSV
## License
Indel Mapper is licensed under Version 3 of the GNU General Public License.