diff --git a/bin/hicstuff_docker/Dockerfile b/bin/hicstuff_docker/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..96d0c54d251b617b9187c388b2c3d4105894c44c --- /dev/null +++ b/bin/hicstuff_docker/Dockerfile @@ -0,0 +1,39 @@ +FROM conda/miniconda3 + +LABEL Name=hicstuff Version=3.2.3 + +RUN echo "deb http://archive.debian.org/debian stretch main contrib non-free" > /etc/apt/sources.list + +RUN apt-get update && apt-get install -y procps bash git + +RUN conda update -y -n base -c defaults conda \ +&& git clone https://github.com/koszullab/hicstuff.git \ +&& cd hicstuff \ +&& git checkout v3.2.3 \ +&& conda init \ +&& conda config --add channels r \ +&& conda config --add channels defaults \ +&& conda config --add channels conda-forge \ +&& conda config --add channels bioconda \ +&& conda create -y -n hicstuff +SHELL ["conda", "run", "-n", "hicstuff", "/bin/bash", "-c"] +RUN conda install -c conda-forge -y \ + pairtools \ + pip \ + bowtie2 \ + minimap2 \ + bwa \ + samtools \ + htslib \ + cooler \ +&& conda clean -afy \ +&& cd hicstuff \ +&& sed -i 's/pairtools//g' requirements.txt \ +&& pip install -Ur requirements.txt \ +&& pip install pysam cython \ +&& pip install . \ +#&& pip install pairtools \ +&& chmod -R +x /usr/local/lib/python3.10/ \ +&& chmod -R +x /usr/local/lib/python3.10/lib-dynload/ \ +&& echo "conda activate hicstuff" >> /root/.bashrc +ENV PATH /usr/local/envs/hicstuff/bin:/usr/local/condabin:$PATH diff --git a/bin/hicstuff_docker/hicstuff_repo b/bin/hicstuff_docker/hicstuff_repo new file mode 120000 index 0000000000000000000000000000000000000000..83d51840ef71d4c415cb41ea5ccd21ada1ced17d --- /dev/null +++ b/bin/hicstuff_docker/hicstuff_repo @@ -0,0 +1 @@ +../hicstuff_repo \ No newline at end of file diff --git a/bin/hicstuff_docker/requirements.txt b/bin/hicstuff_docker/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..65b4ed1638a22ebecc9a2bfb80a6c3d97a88ab0f --- /dev/null +++ b/bin/hicstuff_docker/requirements.txt @@ -0,0 +1,12 @@ +numpy +scipy +pandas >= 1.5.0 +matplotlib >= 3.4.0 +docopt +biopython +requests +scikit-learn +pysam +pyfastx +cooler +pairtools