Docker 4.6.1.0 image not finding includes

[pjgreer]

First, thank you all for your hard work.

I would like to submit a bug in the latest docker image.

I use the gatk docker image as a base for some analyses I perform. I recently tried to update from 4.5.0.0 to the 4.6.1.0 image and I get errors compiling htslib via the installed miniconda gcc. The error is that configure does not find the zlib.h include even though it is there when I do a find command. If I use the 4.6.0.0 image or any prior image, htslib compiles correctly.

Using the below docker recipe, docker build works for gatk:4.6.0.0, but if you change the FROM image file to gatk:4.6.1.0 or gatk:latest the configure step fails. I am running this on an ubuntu 22 vm on gcp.

-Phil

FROM broadinstitute/gatk:4.6.0.0

RUN curl -O https://packages.cloud.google.com/apt/doc/apt-key.gpg && \
    apt-key add apt-key.gpg && apt-get update && \
    apt-get install -y  build-essential gcc wget make autoconf zlib1g-dev libncurses5-dev libncursesw5-dev liblzma-dev libbz2-dev && \
    apt-get install -y unzip git cmake libcurl4-openssl-dev parallel python3-pip libssl-dev zlib1g-dev 

ENV HTSLIB_CONFIGURE_OPTIONS="--enable-gcs --enable-libcurl"
ENV HTSLIB_LIBRARY_DIR=/usr/local/lib
ENV HTSLIB_INCLUDE_DIR=/usr/local/include:/usr/include
ENV HTSLIB_SOURCE=/htslib-1.15.1

RUN conda update -y conda
RUN conda init


RUN wget https://github.com/samtools/htslib/releases/download/1.21/htslib-1.21.tar.bz2 && \
    tar xjf htslib-1.21.tar.bz2 && \
    cd htslib-1.21 && \
    env && \
    cpp -v /dev/null -o /dev/null && \
    ./configure --enable-gcs --enable-libcurl && \
    make && \
    make install && \
    cd ..  

CMD "bash"