vimalkvn/cutadapt repository overview

⁠A docker image for cutadapt

This is the source repository for the docker image vimalkvn/cutadapt⁠.

⁠Notes

1. This image has cutadapt⁠ version 1.13 installed.

2. The python 3.5-slim docker image is used as a base.

3. To run this container, use the run-cutadapt⁠ wrapper script like this:

    ./run-cutadapt -a CTGTCTCTTATACACATCTGACGCTGCCGACGA \
    -o output.fastq input.fastq
   

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   or run the container directly like this:

    docker run --rm -v $(pwd):/data -w /data -e LOGNAME=$(logname) \
    -e USER=$(logname) -u ${UID}:${UID} vimalkvn/cutadapt \
    -a CTGTCTCTTATACACATCTGACGCTGCCGACGA -o output.fastq input.fastq
   

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   The -e and -u options are used so that the container has permissions to read input files and the generated output files will be owned by the user running the container and not root. Default user is cutadapt.

   If you are using one of the methods above, input files are assumed to be present in the directory where the command is run.

   Other cutadapt options can be specified and are sent as is.

   User must have either:

   • sudo access to run this script (script should be run as sudo run-cutadapt) or the

   • user must be part of the docker group.