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##DOCKER FILE

FROM debian:wheezy

COPY jdk1.8.0_45 jdk1.8.0_45

ADD IO.class IO.class

ADD CopyNLines.class CopyNLines.class

RUN update-alternatives --install /usr/bin/java java /jdk1.8.0_45/bin/java 100

RUN update-alternatives --install /usr/bin/java java /jdk1.8.0_45/bin/javac 100

##Some use informations/recommendations

###To use this tool you should run the following command:

docker run -v /host/path/:/container/path/:rw ngspipes/copynlines java CopyNLines src target nLines

###Notes:

  • /host/path/: folder must have adapters of trimmomatic you want to use and all de data you need to use while running the trimmomatic tool.

  • /container/path/: directory path inside docker container to communicate directly with /host/path/.

We recommend to define output parameters /container/path/target.

Usage: src target [nLines]

  • src: file source of the data to be copied
  • target: file destination for data copied
  • nLines: optional arguments, especify a number of lines to be copied. Default value all lines

###Example for usecase:

docker run -v /home/results/:/output/:rw ngspipes/copynlines /output/srcFile.fastq /output/targetFile.fastq 20

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ngspipes

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