https://github.com/p2m2/service-flask-thermorawfileparser-openms
A simple HTML interface for converting RAW format to MzML, MzXML, and MGF files.
https://github.com/p2m2/service-flask-thermorawfileparser-openms
flask metabolomics openms thermofileparser
Last synced: 5 months ago
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A simple HTML interface for converting RAW format to MzML, MzXML, and MGF files.
- Host: GitHub
- URL: https://github.com/p2m2/service-flask-thermorawfileparser-openms
- Owner: p2m2
- Created: 2024-04-05T15:00:04.000Z (about 2 years ago)
- Default Branch: main
- Last Pushed: 2025-02-04T12:17:08.000Z (over 1 year ago)
- Last Synced: 2025-02-04T13:24:02.663Z (over 1 year ago)
- Topics: flask, metabolomics, openms, thermofileparser
- Language: Python
- Homepage:
- Size: 29.3 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: Readme.md
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README
## service-flask-thermorawfileparser-openms
[](https://services-p2m2-test-192-168-100-66.vm.openstack.genouest.org)
[](https://services-p2m2-test-192-168-100-66.vm.openstack.genouest.org)
A simple HTML interface for converting RAW format to MzML, MzXML, and MGF files.
### Install
```bash
python3 -m venv env
. env/bin/activate
pip3 install -r requirements.txt
```
### Configuration
Edit `.flaskenv` to configure the Flask environment variables.
#### production
```
FLASK_APP = app
FLASK_DEBUG = False
FLASK_TESTING = False
FLASK_RUN_HOST="0.0.0.0"
FLASK_RUN_PORT="80"
FLASK_ENV=production
```
### Run service
```bash
. .venv/bin/activate
flask run
```
##### production
```bash
sudo su root
python3 -m venv env
. env/bin/activate
pip3 install -r requirements.txt
nohup flask run > log.txt 2>&1 &
```
Visit `http://{host}:{port}/` to access the service.
## Docker images
### inraep2m2/Dockerfile_thermorawfileparser
version : ThermoRawFileParser1.4.3.zip
#### Build and push image
```bash
docker build . -f Dockerfile_thermorawfileparser -t inraep2m2/thermorawfileparser:1.4.3
docker login --username=p2m2
docker image push inraep2m2/thermorawfileparser:1.4.3
```
#### Usage
```bash
raw data is localized in $PWD/data directory
docker run -v $PWD/data:/data -t inraep2m2/thermorawfileparser:1.4.3 -i=/data/MM_NOx_1_Direct.raw
```
### inraep2m2/openms
[Original Dockerfile](https://raw.githubusercontent.com/OpenMS/dockerfiles/master/executables/Dockerfile)
#### Build and push image
```bash
docker build . -f Dockerfile_openms -t inraep2m2/openms:3.1.0-pre-nightly-2024-02-03
docker login --username=p2m2
docker image push inraep2m2/openms:3.1.0-pre-nightly-2024-02-03
```
#### Usage
```bash
raw data is localized in $PWD/data directory
docker run -v $PWD/data:/data -it inraep2m2/openms:3.1.0-pre-nightly-2024-02-03 FileConverter -in /data/MM_NOx_1_Direct.mzML -out /data/MM_NOx_1_Direct.mzXML
```