Tool to copy files required for coverage assessment for the TruSight Cancer analysis. Renames the directories created with numbers in front in the order of the samples on the worksheet created in Shire (e.g. 01 20M01234)
This software uses Python 3.7.
It has dependencies which are recommended to be installed using a Conda environment. Install Conda:
https://docs.conda.io/projects/conda/en/latest/user-guide/install/download.html
Clone the repository:
git clone https://github.com/AWGL/copy_tsca
Create Conda environment:
conda env create -f tsca_copy.yml
Set up the config file to point to the correct locations on the local computer:
Edit config.py and save as config.py
The code can then be run after the Conda environment is activated:
python copy_tsca.py
The software needs to be packaged to run on imaged PCs without Python installed. The package needs to be built on a Windows 7 PC with Python 3.7 installed.
Install pyinstaller if it is not already installed:
conda install pyinstaller
Package the software:
pyinstaller copy_tsca.py
Copy the dist directory generated by pyinstaller to the PC or shared drive from which the sofware is to be run.
It may be useful to create a shortcut to the executable file copy_tsca.exe for the user.
Double click on the copy_tsca.exe file.
-
Wait for a pop-up box called "TSCa File Copy Data Entry" to appear, enter the run identifier in the pop-up box and click OK
-
Wait for a second pop-up box with logging information to appear. This box is called "TSCa File Copy Information" and read the message.
- If the message indicates that the software has finished correctly, the files and directories have been created.
- If there is an error message displayed, the software has not executed correctly, click OK and perform troubleshooting.
A log file tsca_copy.log is generated at each execution of the software to aid troubleshooting
- None
In case the Conda environment build fails.
- python 3.7
- tkinter