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Last pushed: a year ago
Short Description
Trimmomatic: A flexible read trimming tool for Illumina NGS data (v0.33)
Full Description

FROM debian:wheezy

ADD trimmomatic-0.33.jar trimmomatic-0.33.jar

COPY jdk1.8.0_45 jdk1.8.0_45

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/trimmomatic0.33 java -jar trimmomatic-0.33.jar [trimmomatic arguments]


  • /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/outputParameterValue.

###Example for usecase:

docker run -v /home/result/:/output/:rw ngspipes/trimmomatic0.33 java -jar trimmomatic-0.33.jar SE -phred33 inputFile.fastq /output/outputFile.fastq ILLUMINACLIP:/output/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

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