Matlab package for image processing and base calling

PuckCaller needs a public toolset bftools for image conversion. You could download bftools at: https://docs.openmicroscopy.org/bio-formats/5.7.1/users/comlinetools/index.html

Unzip the package and put it under your directory.

Java is required to run bftools.

For Windows:

1. Download PuckCaller Windows package;
2. Prepare manifest file;
3. Open Matlab;
4. Set PuckCaller script folder as current folder;
5. Open PuckCaller.m;
6. Click "Run" or "Run Section".

For Linux:

1. Download PuckCaller Linux package;
2. Compile matlab code (command might be different on your system):

	use .matlab-2019a
	mcc -m PuckCaller.m -a PuckCaller_script_folder -d PuckCaller_script_folder -o PuckCaller

3. Modify PuckCaller_script_folder/run_PuckCaller.sh

	reuse Java-1.8 (or another version)
	manifest=$2
	eval "\"{$PuckCaller_script_folder}\"" ${manifest}

4. Prepare manifest file;
5. Run PuckCaller:

	qsub -o logfile -l h_vmem=30g -l h_rt=10:0:0 -j y PuckCaller_script_folder/run_PuckCaller.sh matlab_path manifest_file

Notice:

1. matlab_path is like /Linux/redhat_7_x86_64/pkgs/matlab_2019a;
2. Check example.manifest.txt for manifest file format;
3. See example run_PuckCaller.sh;
4. See user_doc.txt for detailed usage of PuckCaller;
5. Email to [email protected] for questions.