diff --git a/docker/lofreq/Dockerfile b/docker/lofreq/Dockerfile new file mode 100644 index 0000000..01ef8de --- /dev/null +++ b/docker/lofreq/Dockerfile @@ -0,0 +1,59 @@ +FROM --platform=linux/amd64 ubuntu:22.04 + +# build time variables +ARG BUILD_DATE="000000" +ENV BUILD_DATE=${BUILD_DATE} +ARG BUILD_TAG="000000" +ENV BUILD_TAG=${BUILD_TAG} +ARG REPONAME="000000" +ENV REPONAME=${REPONAME} + +LABEL maintainer + +# Create Container filesystem specific +# working directory and opt directories + +# This section installs system packages required for your project +# If you need extra system packages add them here. +RUN apt-get update \ + && apt-get -y upgrade \ + && DEBIAN_FRONTEND=noninteractive apt-get install -y \ + automake \ + build-essential \ + curl \ + git \ + gcc \ + libbz2-dev \ + libcurl4-gnutls-dev \ + libgsl0-dev \ + libperl-dev \ + liblzma-dev \ + libncurses5-dev \ + libssl-dev \ + python3-dev \ + zlib1g-dev + +RUN ln -s /usr/bin/python3.10 /usr/bin/python + +WORKDIR /opt2 + +ARG htsversion=1.19 + +RUN curl -L https://github.com/samtools/htslib/releases/download/${htsversion}/htslib-${htsversion}.tar.bz2 | tar xj \ + && cd htslib-${htsversion} \ + && ./configure \ + && make \ + && make install + +RUN curl -L https://github.com/samtools/bcftools/releases/download/${htsversion}/bcftools-${htsversion}.tar.bz2 | tar xj \ + && cd bcftools-${htsversion} \ + && ./configure && make && make install + +RUN git clone https://github.com/CSB5/lofreq \ + && cd lofreq \ + && ./bootstrap \ + && ./configure --with-htslib=/usr/local \ + && make \ + && make install + +ENV LD_LIBRARY_PATH /usr/local/lib:$LD_LIBRARY_PATH diff --git a/docker/lofreq/build.sh b/docker/lofreq/build.sh new file mode 100644 index 0000000..4f87a24 --- /dev/null +++ b/docker/lofreq/build.sh @@ -0,0 +1,11 @@ +# Build image + +docker build --platform linux/amd64 --tag ccbr_logan_base:v0.3.4 -f Dockerfile . + +docker tag ccbr_lofreq:v0.0.1 dnousome/ccbr_lofreq:v0.0.1 +docker push dnousome/ccbr_lofreq:v0.0.1 + +docker push dnousome/ccbr_logan_base:latest + + +