Add a Docker container

Dockerfiles/Dockerfile.fastp

@@ -0,0 +1,56 @@
+############# 
+# Dockerfile to build container image for fastp : a bionformatics NGS QC/adapter-trim  tool
+# See Docs and Source code at:  https://github.com/OpenGene/fastp
+# Example unix cmdline and parameters:
+#      fastp -i raw.fq -o ./clean.fq  -h "<samplename>-fastp_report" -w12 -e 25 -l 40 -y -5 -3 -W4 -M20  \ 
+#                --overrepresentation_analysis -P 100 --dont_eval_duplication -x 
+# Build Image with (and specify tagged version):
+#    docker build --build-arg FP_VERSION=0.23.4  -t fastp:0.23.4  -f ./Dockerfile.fastp .
+#
+# OR to change the build user id to run as yourself, do this:
+#    export myUID=$(id -u) ; export myGID=$(id -g)     # See below for details setting the user
+#    docker build --build-arg USER=$myUID:$myGID  FP_VERSION=0.23.4 -t fastp:0.23.4  -f ./Dockerfile.fastp .
+# Run in iteractive mode like:
+#    docker run -it --rm --network="host" --cpus=2 -m 64000m -v ${PWD}:${PWD} -w ${PWD}  --entrypoint /bin/bash   my_image  
+#    ... where "my_image" is the full length image name (i.e: fastp:latest) or the specific "IMAGE ID" in your docker setup (docker image ls)
+# OR run as default and it will use the internal entrypoint: 
+#    docker run -it --rm --network="host" -v ${PWD}:${PWD} -w ${PWD}  my_image  --flags
+#    Here is a full example with flags, running within the Docker:
+#     /app/fastp -i testsample-pairsR1.fq.gz -I testsample-pairsR2.fq.gz -R testsample_fastP -h testsample.fastp_report.html 
+#      --thread 12 --detect_adapter_for_pe --dedup --dup_calc_accuracy 4 -e 25 -l 35 --trim_poly_g --trim_poly_x -p -P 100
+#############
+
+# FROM scratch
+FROM ubuntu:20.04
+LABEL org.opencontainers.image.authors="[email protected]"
+
+ARG DEBIAN_FRONTEND="noninteractive"
+ARG TZ="UTC"
+ENV TZ="${TZ}"
+
+# Update the repository sources list
+RUN apt-get update && apt-get install -y \
+    wget \
+    nano \
+    && apt-get clean  && rm -rf /var/lib/apt/lists/*
+
+
+# Verified version of 'fastp' to use.   0.23.4 as of Q3 2023.  Provide as cmdline argument to override. Assumes a Linux 64bit ELF binary
+ARG FP_VERSION=0.23.4
+
+# Get the precompiled package version wanted
+#  fastp v0.23.4
+WORKDIR /app
+RUN  wget http://opengene.org/fastp/fastp.${FP_VERSION} \
+    && mv fastp.${FP_VERSION} fastp \
+    && chmod a+x ./fastp  
+
+# Set run user/group as myUID 2000 myGID 3000 for use in Kubernetes (and avoid running as root)
+ARG USER=appuser
+ARG USERGROUP=appgroup
+ARG myUID=2000
+ARG myGID=3000
+RUN groupadd -r -g ${myGID} ${USERGROUP}  &&  useradd -g ${myGID} --myUID=${myUID} ${USER}
+# USER appuser:appgroup
+USER ${myUID}:${myGID}
+ENTRYPOINT ["/app/fastp"]

README.md

@@ -105,6 +105,15 @@ wget http://opengene.org/fastp/fastp.0.23.1
 mv fastp.0.23.1 fastp
 chmod a+x ./fastp
 ```
+
+## Use a Docker container 
+The image is built with Ubuntu 20.04 as base.  See Dockerfile.fastp in Dockerfiles folder
+```shell
+git clone https://github.com/OpenGene/fastp.git
+export FP_VERSION="0.23.4"
+docker build --build-arg BUILDKIT_INLINE_CACHE=1 --build-arg FP_VERSION=${FP_VERSION} --tag fastp:${FP_VERSION} --file ./Dockerfiles/Dockerfile.fastp  .
+```
+
 ## or compile from source
 `fastp` depends on `libdeflate` and `libisal`, while `libisal` is not compatible with gcc 4.8. If you use gcc 4.8, your fastp will fail to run. Please upgrade your gcc before you build the libraries and fastp.