readme update

README.md

@@ -11,4 +11,23 @@ git clone --recurse-submodules https://git-r3lab.uni.lu/susheel.busi/ont_pilot_g
 
 [About git submodules](https://git-scm.com/book/en/v2/Git-Tools-Submodules)
 
-TODO: other dependencies
+TODO: other dependencies ???
+
+# Analysis
+
+## On LCSB HPC server `iris`
+
+Main `conda` environment: `/scratch/users/vgalata/miniconda3/ONT_pilot`
+
+Example commands for `GDB`:
+
+```bash
+# conda
+conda activate /scratch/users/vgalata/miniconda3/ONT_pilot
+# analysis: check which rules will be executed
+snakemake -s workflow/Snakefile --configfile config/GDB/config.yaml --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline --cores 1 -rpn
+# submit jobs using slurm
+./config/GDB/sbatch.sh
+# report
+snakemake -s workflow_report/Snakefile --configfile config/GDB/config.yaml --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline --cores 1 -rpn
+```
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