This project is intend to monitor the staus of files and data that are submitted to DCC. It can pull back feedback of submitted xml files; data of submitted procedure (including specimen, lines etc); and media files. As of today, all IMPC part and EBI procedure part has been implemented and well tested. EBI images needs some more work.
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- Python 3.x
- Git
- pip3
First, open your terminal/command prompt and cd to your work directory, then create a virtual environment in Python 3.8+. Use the following command if you like to use venv just like me:
python3 -m venv .env/venv_name
. You can also use conda or pyenv, whatever you like. Next, activate your virtual environment use the following command:
. .env/venv_name/bin/activate
. In your work directory, run the following command to download the repository:
git clone https://github.com/TheJacksonLaboratory/FetchDCCResult.git
. Now, you need to install the dependencies of the application, to do that, use the following command:
pip install -r requirements.txt
Using application is quite straightfoward, but before you use it, please make sure that you have enviormrnt setup for bash/shell. If you are on a Mac/Linux machine like me, you are fine. If you are on a windows machine, please use this link to have your enviroment setup. After everything is configured, run the following commands on your terminal:
```
chmod +x /path/to/your/directory/impc.sh
./path/to/your/directory/impc.sh
```
impc.sh will execute all tasks for you. If you are on a windows machine, open your command prompt and run the following command:
```
/path/to/your/directory/impc.bat
```
Replace name of Bash\Batchfile script from "impc" to "ebi" if you would like to get feedback of submitted procedures from EBI. Currently, this app is scheduled to run weekly on bhwin0236.jax.org.