diff --git a/Dockerfile b/Dockerfile index 795f623..c8b4bb6 100644 --- a/Dockerfile +++ b/Dockerfile @@ -49,6 +49,15 @@ RUN python3 -m pip install --upgrade pip RUN pip uninstall easypqp \ && pip install git+https://github.com/Nesvilab/easypqp.git@master \ && pip install lxml + +RUN apt-get update && \ + apt-get install -y ncbi-blast+ + +# Install latest seqkit +RUN wget https://github.com/shenwei356/seqkit/releases/download/v2.9.0/seqkit_linux_amd64.tar.gz && \ + tar -zxvf seqkit_linux_amd64.tar.gz && \ + mv seqkit /usr/local/bin/ && \ + rm seqkit_linux_amd64.tar.gz # create a directory with 777 permission and set it to the work directory RUN mkdir /fragpipe_bin @@ -60,8 +69,8 @@ RUN mkdir tmp RUN chmod 777 tmp # download and install fragPipe -RUN wget https://github.com/Nesvilab/FragPipe/releases/download/23.1/FragPipe-23.1-linux.zip -P fragPipe-23.1 -RUN unzip fragPipe-23.1/FragPipe-23.1-linux.zip -d fragPipe-23.1 +RUN wget https://github.com/Nesvilab/FragPipe/releases/download/22.0/FragPipe-22.0.zip -P fragPipe-22.0 +RUN unzip fragPipe-22.0/FragPipe-22.0.zip -d fragPipe-22.0 RUN chmod -R 777 /fragpipe_bin # set environment variables @@ -69,11 +78,10 @@ ENV JAVA_HOME="/usr/lib/jvm/java-17-openjdk-amd64/" RUN export JAVA_HOME # copy Fragpipe dependencies - -COPY MSFragger-4.3.jar /fragpipe_bin/fragPipe-23.1/fragpipe-23.1/tools/MSFragger-4.3.jar -COPY diaTracer-1.3.3.jar /fragpipe_bin/fragPipe-23.1/fragpipe-23.1/tools/diaTracer-1.3.3.jar -COPY IonQuant-1.11.11.jar /fragpipe_bin/fragPipe-23.1/fragpipe-23.1/tools/IonQuant-1.11.11.jar +COPY MSFragger-4.1.jar /fragpipe_bin/fragPipe-22.0/fragpipe/tools/MSFragger-4.1.jar +COPY diaTracer-1.1.5.jar /fragpipe_bin/fragPipe-22.0/fragpipe/tools/diaTracer-1.1.5.jar +COPY IonQuant-1.10.27.jar /fragpipe_bin/fragPipe-22.0/fragpipe/tools/IonQuant-1.10.27.jar WORKDIR /rocker-build/ -ADD Dockerfile . \ No newline at end of file +ADD Dockerfile . diff --git a/README.md b/README.md index 4c8efa4..91b71fd 100644 --- a/README.md +++ b/README.md @@ -14,12 +14,12 @@ git clone git@github.com:rokitalab/fragpipe.git 2. Pull the docker container: ``` -docker pull pgc-images.sbgenomics.com/rokita-lab/fragpipe:latest +docker pull pgc-images.sbgenomics.com/rokita-lab/fragpipe:v22.0 ``` 3. Start the docker container, from the root directory, run: ``` -docker run --name -d -e PASSWORD=ANYTHING -p 8787:8787 -v $PWD:/home/rstudio/fragpipe pgc-images.sbgenomics.com/rokita-lab/fragpipe:latest +docker run --name -d -e PASSWORD=ANYTHING -p 8787:8787 -v $PWD:/home/rstudio/fragpipe pgc-images.sbgenomics.com/rokita-lab/fragpipe:v22.0 ``` Note: If running on a Macbook with M1 chip, include the argument `--platform linux/amd64`