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:
- Download PuckCaller Windows package;
- Prepare manifest file;
- Open Matlab;
- Set PuckCaller script folder as current folder;
- Open
PuckCaller.m; - Click "
Run" or "Run Section".
For Linux:
- Download PuckCaller Linux package;
- 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
- Modify
PuckCaller_script_folder/run_PuckCaller.sh
reuse Java-1.8 (or another version)
manifest=$2
eval "\"{$PuckCaller_script_folder}\"" ${manifest}
- Prepare manifest file;
- 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:
- matlab_path is like
/Linux/redhat_7_x86_64/pkgs/matlab_2019a; - Check
example.manifest.txtfor manifest file format; - See example
run_PuckCaller.sh; - See
user_doc.txtfor detailed usage of PuckCaller; - Email to
puckcaller@gmail.comfor questions.