Using docker with SoS

In the following example, a docker image compbio/ngseasy-fastqc:1.0-r001 is used to process local fastq files



In [1]:

    
%run --fastq_files data/*.fastq

parameter: fastq_files = paths
input: fastq_files

sh: container='compbio/ngseasy-fastqc:1.0-r001', expand=True     
    /usr/local/bin/fastqc {_input}









    




Pulling docker image compbio/ngseasy-fastqc:1.0-r001






    



Started analysis of S20_R1.fastq
Analysis complete for S20_R1.fastq
Started analysis of S20_R2.fastq
Analysis complete for S20_R2.fastq



In [2]:

    
%rerun --fastq_files data/*.fastq -n









    




docker run --rm   -v /Users/bpeng1/sos/JupyterCon2018:/Users/bpeng1/sos/JupyterCon2018 -v /Users/bpeng1/sos/JupyterCon2018/tmpbjy4o06j/docker_run_98331.sh:/var/lib/sos/docker_run_98331.sh    -t  -w=/Users/bpeng1/sos/JupyterCon2018 -u 1985961928:895809667    compbio/ngseasy-fastqc:1.0-r001 /bin/sh /var/lib/sos/docker_run_98331.sh






    



/usr/local/bin/fastqc /Users/bpeng1/sos/JupyterCon2018/data/S20_R1.fastq /Users/bpeng1/sos/JupyterCon2018/data/S20_R2.fastq



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