/ - Diff - BIOI2 Formations - Forge Logicielle I2BC

« Previous | Next »

Revision 1e5111ea

initial commit - exercise0

     samples=["P10415", "P01308"]
     rule targets:
         input:
             expand("fasta/{sample}.fasta", sample=samples),
             "fusionFasta/allSequences.fasta",
             "mafft/mafft_res.fasta",
     rule loadData:
         output:
             "fasta/{sample}.fasta",
         log:
             stdout = "logs/{sample}_wget.stdout",
             stderr = "logs/{sample}_wget.stderr",
         params:
             dirFasta = "fasta",
         threads: 1
         shell:
             """
               wget --output-file {log.stderr} \
                    --directory-prefix {params.dirFasta} \
                    https://www.uniprot.org/uniprot/{wildcards.sample}.fasta > {log.stdout}
             """
     rule fusionFasta:
         input:
             expand("fasta/{sample}.fasta", sample=samples),
         output:
             "fusionFasta/allSequences.fasta",
         log:
             "logs/fusionData.stderr",
         threads: 1
         shell:
             """
                 cat {input} > {output} 2> {log}
             """
     rule mafft:
         input:
             rules.fusionFasta.output,
         output:
             "mafft/mafft_res.fasta",
         log:
             "logs/whichMafft.txt",
         threads: 1
         shell:
             """
                 mafft {input} > {output} 2> {log}
             """

     Pour faire fonctionner le pipeline il faut se connecter sur un noeud du cluster puis:
     - charger l'environnement snakemake:
     module load snakemake/snakemake-8.4.6
     module load nodes/mafft-7.475
     - executer le programme:
     snakemake --cores 4

Also available in: Unified diff