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2 hours ago by

I'm new to docker technology, I'm trying to run the exceRpt small RNA pipeline. I've pulled the image rkitchen/excerpt .

rkitchen/excerpt                           latest              38fceb372de2        2 years ago         2.02GB

I want to call on the image for each fastq file in my data directory so I have a file called runexrpt with the following contet:

   for i in /data/projects/0938_Feroz_Auyeung/test_fastq
do
    echo $i
    docker run -v /data/projects/0938_Feroz_Auyeung/test_fastq:/exceRptInput
 
        -v /data/projects/0938_Feroz_Auyeung/excerptOuts_all:/exceRptOut
 
        -v /data/genomes/exceRpt_hg38:/exceRpt_DB/hg38 
        -t rkitchen/excerpt 
        INPUT_FILE_PATH=/exceRptInput/$(basename $i) 
        ENDOGENOUS_LIB_PRIORITY=miRNA,tRNA,gencode,piRNA,circRNA 
        MAIN_ORGANISM_GENOME_ID=hg38 
        ADAPTER_SEQ=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 
        N_THREADS=20 
        JAVA_RAM=32G 
        MIN_READ_LENGTH=12 
done
echo "finished"

when I use docker run
runexrpt
it tells me that the image doesn't exist, I understand that the error arises because the image I have is rkitchen/excerpt, so my question is how would I run this image so that all my fastq files in the fastq folder are passed through the rkitchen/excerpt image? Do I make the above chunk of code into a new docker image using the docker build command and run that to make the container that will pass all fastq files into the pipeline and give me all their outputs?

any help/guidance would be appreciated, thank you!



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