Made the snakemake implementation more generic and updated the readme

Projects/AlPhaPha/2024/ReadMe.md

@@ -16,3 +16,20 @@ cmake -DCMAKE_EXPORT_COMPILE_COMMANDS=1
 
 ## Do not forget
 In project config modifiy analysis output before doing a test analysis
+
+# Config NPTOOL
+when doing cmake for npl do -DNPMULTITHREADING=0 to facilitate multithreading
+with snakemake
+
+# Config for SnakeMake
+ 
+You *NEED* Python3.12
+
+## venv 
+```
+python3.12 -m venv ./.venv
+source ./.venv/bin.activate
+pip install snakemake
+```
+
+Your project.config must point to the root dir of your computer

Projects/AlPhaPha/2024/Snakefile

@@ -3,7 +3,7 @@ import subprocess
 
 # Lire le répertoire d'entrée depuis les arguments de configuration
 #input_directory = config["folder"]
-input_directory = "/home/efremovt/bin/nptool/Projects/AlPhaPha/DataMacro/output/"
+input_directory = os.getcwd() + "/../DataMacro/output"
 origin = [] 
 # Iterate over files in input_directory
 for filename in os.listdir(input_directory):
@@ -12,14 +12,14 @@ for filename in os.listdir(input_directory):
     origin.append(filename)
 
 # Définir le répertoire de sortie pour les fichiers convertis
-phy_directory = "/home/efremovt/bin/nptool/Projects/AlPhaPha/DataMacro/output/analysis"
+phy_directory = os.getcwd() + "/../DataMacro/output/analysis"
 #phy_directory = "./"
 
 # define target files directory
 analysedfile = []
 for inputfile in origin:
   #analysedfile.append("/home/morfouacep/Physics/NPTool/nptool/Projects/ana_e850/root/analysis/"+inputfile.replace("_raw_","_"))
-  analysedfile.append("/home/efremovt/bin/nptool/Projects/AlPhaPha/DataMacro/output/analysis/"+inputfile)
+  analysedfile.append( os.getcwd() + "/../DataMacro/output/analysis/"+inputfile)
 
 ## batch rules
 rule all:

Projects/AlPhaPha/2024/convert_snakemake.sh

 #!/bin/bash
 echo "- executing snakemake file for npanalysis..."
-snakemake --cores 8 --forceall --keep-incomplete --keep-going --rerun-incomplete
+snakemake --cores 30 --forceall --keep-incomplete --keep-going --rerun-incomplete
 echo "- snakemake executed successfully!"
 echo "- Merging file..."
 root -q '../DataMacro/Merger.C(16,"root/analysis","VamosCalib241","../DataMacro/output/analysis/run_raw_241_")'