feat: add lofreq container

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=${REPONAME}
+
+LABEL maintainer <nousomedr@nih.gov>
+
+# Create Container filesystem specific 
+# working directory and opt directories 
+
+# This section installs system packages required for your project
+# If you need extra system packages add them here.
+RUN apt-get update \
+ && apt-get -y upgrade \
+ && DEBIAN_FRONTEND=noninteractive apt-get install -y \
+      automake \
+      build-essential \
+	curl \
+      git \
+      gcc \
+	libbz2-dev \
+	libcurl4-gnutls-dev \
+	libgsl0-dev \
+    	libperl-dev \
+	liblzma-dev \
+	libncurses5-dev \
+	libssl-dev \
+      python3-dev \
+	zlib1g-dev 
+
+RUN ln -s /usr/bin/python3.10 /usr/bin/python
+
+WORKDIR /opt2 
+
+ARG htsversion=1.19
+
+RUN curl -L https://github.com/samtools/htslib/releases/download/${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

docker/lofreq/build.sh

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+# 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
+
+
+