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runme.sh

+# for Hubbers
+
+#install conda via miniconda :
+follow this tuto : https://docs.conda.io/en/latest/miniconda.html#linux-installers
+
+#create your conda env
+conda create -n snakemake 
+conda activate snakemake
+conda config --add channels defaults
+conda config --add channels bioconda
+conda config --add channels conda-forge
+conda install -c anaconda python
+conda install -c bioconda snakemake 
+conda install -c anaconda pandas
+conda install -c bioconda pysam
+conda install -c conda-forge singularity
+
+#run the workflow:
+module load fastqc
+module load samtools/1.10
+module load bedtools/2.29.2
+module load cutadapt-devel/2.10 cutadapt/2.10
+module load bowtie2/2.3.5.1
+module load STAR/2.7.3a
+module load subread/2.0.0
+module load deepTools/3.4.1
+module load MultiQC/1.9
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