add README.md

README.md

+# GENTOOLS: Suite of workflows for gentic data processing
+
+## Installation
+
+Pull the current repo with git pull. Then run the following in an environment where conda is available:
+
+```
+cd gentools/
+. .set.sh
+conda create -n gentools -c conda-forge -c bioconda pysam snakemake=7 pyvcf pandas  py_fasta_validator
+conda activate gentools
+```
+
+
+Snakemake v8 is supported for BAMQCs and CNV_Call workflows.
+
+
+## Running
+
+### Snakemake v7
+
+
+``` 
+snakemake -s <path to smk file> \ # in the directory workflow
+    --configfile <your config file> \ # example can be found in the workflow directory
+    --cluster '<your sbatch command>' \ # on glicid can be something like : 'sbatch --qos=medium --time=32:00:00 --mem=10g --cluster=nautilus -e error.myWF.txt'
+    -j 10 \ # or more, depending on your queue
+    --use-conda   
+```
+
+### Snakemake v8 
+
+```
+snakemake -s <path to smk file> \ # in the directory workflow
+    --configfile <your config file> \ # example can be found in the workflow directory
+    --profile '<your profile>' \ # In BAMQCs and CNV_Call contain adapted profile directories 
+    -j 10 \ # or more, depending on your queue
+    --use-conda 
+```
+
+### Glicid & conda
+
+/!\ snakemake doesnot manage micromamba environments. In order to use gentools on Glicid with micromamba there are 2 options:
+
+1) Install mamba
+
+You can use `micromamba install mamba`. Snakemake should then run normally as long as mamba is available
+
+2) Install all dependencies (recommended)
+
+A less messy way to proceed is to launch your snakemake WF from an environment were all dependencies are available.