From 4ecff2dd6d05e5cb41144495f7ebe28f0d881697 Mon Sep 17 00:00:00 2001
From: scarlet <scarlet@MinION-2>
Date: Tue, 27 Jul 2021 18:15:16 +0200
Subject: [PATCH] add docker file

---
 dockerfile/Dockerfile | 80 +++++++++++++++++++++++++++++++++++++++++++
 dockerfile/README.md  |  7 ++++
 2 files changed, 87 insertions(+)
 create mode 100644 dockerfile/Dockerfile
 create mode 100644 dockerfile/README.md

diff --git a/dockerfile/Dockerfile b/dockerfile/Dockerfile
new file mode 100644
index 0000000..cceaff2
--- /dev/null
+++ b/dockerfile/Dockerfile
@@ -0,0 +1,80 @@
+## Parent image (first layer)
+FROM biocorecrg/centos-perlbrew-pyenv-java:latest
+#FROM centos/python-36-centos7
+ARG PYTHON_VERSION=3.6.3
+USER root 
+RUN bash
+
+
+## Install wget
+RUN pwd 
+RUN yum -y upgrade
+RUN yum install -y which
+RUN yum -y install wget libcurl-devel
+
+## Install python3.7
+WORKDIR /usr/local/bin
+RUN yum -y install gcc openssl-devel bzip2-devel libffi-devel zlib-devel xz-devel
+RUN wget https://www.python.org/ftp/python/3.6.3/Python-3.6.3.tgz
+RUN tar xzf Python-3.6.3.tgz
+
+WORKDIR /usr/local/bin/Python-3.6.3
+RUN ./configure --enable-optimizations
+RUN yum install make -y
+RUN make altinstall
+RUN echo 'current location'
+
+#RUN rm python3
+WORKDIR /usr/bin
+RUN ln -fs /usr/local/bin/Python-3.6.3/python python3
+#RUN ln -fs /usr/local/bin/Python-3.6.3/python python
+RUN chmod +x python; chmod +x python3
+#RUN ln -fs /usr/local/bin/pip pip3
+
+# Intall pip
+RUN yum -y install epel-release
+RUN curl https://bootstrap.pypa.io/get-pip.py --output get-pip.py
+RUN python3 get-pip.py
+RUN python -m pip install --upgrade pip
+RUN pip3 install requests paho-mqtt
+
+## Install samtools
+WORKDIR /usr/local/bin 
+RUN wget https://sourceforge.net/projects/samtools/files/samtools/1.3/samtools-1.3.tar.bz2
+RUN tar xjf samtools-1.3.tar.bz2
+RUN ls -lrt 
+RUN pwd
+RUN chmod +x samtools-1.3/configure
+RUN cd samtools-1.3; ./configure ; make; make install
+RUN cd samtools-1.3/htslib-1.3; ./configure ; make
+RUN cd /usr/local/bin ;  ln -fs samtools-1.3/samtools .
+RUN cd /usr/bin/; ln -fs /usr/local/bin/samtools-1.3/samtools samtools 
+
+## Install sam2tsv
+WORKDIR /usr/local/bin
+RUN wget https://github.com/enovoa/EpiNano/raw/master/misc/sam2tsv.jar
+
+## isntall dependencies
+RUN pip3 install --upgrade pip
+RUN pip3 install atomicwrites==1.4.0 attrs==21.2.0 biopython==1.76 cloudpickle==1.3.0
+RUN pip3 install dask==2.5.2 fsspec==2021.6.1 future==0.17.1 h5py==2.10.0 importlib-metadata==4.6.1
+RUN pip3 install locket==0.2.1  more-itertools==8.8.0 numpy==1.17.2 pandas==0.24.2
+RUN pip3 install partd==1.2.0 pluggy==0.13.1 py==1.10.0 pysam==0.15.3 pytest==4.4.1 python-dateutil==2.8.1
+RUN pip3 install pytz==2021.1 scikit-learn==0.20.2 scipy==1.5.4 six==1.16.0 toolz==0.11.1 typing-extensions==3.10.0.0 zipp==3.5.0
+
+
+
+
+### indtall Epinnao
+WORKDIR /usr/local/bin
+RUN git clone --depth 2 https://github.com/enovoa/EpiNano.git
+
+# Remove all archives
+RUN rm -f *.zip *.bz2 *.gz
+
+# create a data folder to process 
+RUN mkdir -p /project/data
+
+#env path
+ENV PATH /usr/local/bin:$PATH
+
diff --git a/dockerfile/README.md b/dockerfile/README.md
new file mode 100644
index 0000000..efcc461
--- /dev/null
+++ b/dockerfile/README.md
@@ -0,0 +1,7 @@
+## run with docker container 
+docker run -it -d --rm --name epivar2 -v "$PWD/xiao_data/":/project/ epi12 python3 /usr/local/bin/EpiNano/Epinano_Variants.py -R /project/ref.fa -b /project/reads.bam -s /usr/local/bin/EpiNano/misc/sam2tsv.jar -n 2
+
+## use singularity and qsub on cluster
+singularity pull docker://huanleliu/epi12
+singularity exec -e /full/path/to/epi12_latest.sif python3 /usr/local/bin/EpiNano/Epinano_Variants.py -R /path/to/ref.fa -b /path/to/reads.bam -s /usr/bin/EpiNano/misc/sam2tsv.jar -n 2
+