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revert docker to fragpipe 22.0 #22

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Merged
rjcorb merged 4 commits into from
Oct 9, 2025
Merged

revert docker to fragpipe 22.0 #22

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7921c58
revert to fragpipe 22.0
rjcorb Sep 23, 2025
7c6b2f9
add ncbi-blast+, seqkit
rjcorb Sep 24, 2025
908e9e3
update README docker instructions
rjcorb Oct 9, 2025
1550be5
correctly install ncbi-blast+
rjcorb Oct 9, 2025
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23 changes: 16 additions & 7 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,16 @@ 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+ wget unzip && \
rm -rf /var/lib/apt/lists/*

# 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
Expand All @@ -60,20 +70,19 @@ 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
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 .
ADD Dockerfile .
4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -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 <CONTAINER_NAME> -d -e PASSWORD=ANYTHING -p 8787:8787 -v $PWD:/home/rstudio/fragpipe pgc-images.sbgenomics.com/rokita-lab/fragpipe:latest
docker run --name <CONTAINER_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`

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