From b6c4350001dc2bb7196d65662ddd63d003cecc8a Mon Sep 17 00:00:00 2001
From: Simone Maestri <simone.maestri@hotmail.it>
Date: Tue, 29 Mar 2022 08:33:57 +0200
Subject: [PATCH] Add Dockerfile

---
 Dockerfile | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 Dockerfile

diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..1dc90e6
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,40 @@
+FROM continuumio/miniconda3
+
+########### set variables
+ENV DEBIAN_FRONTEND noninteractive
+
+########## generate working directories
+RUN mkdir /home/tools
+
+######### dependencies
+RUN apt-get update -qq \
+    && apt-get install -y \
+    build-essential \
+    wget \
+    unzip \
+    bzip2 \
+    git \
+    libidn11* \
+    nano \
+ && apt-get clean \
+ && rm -rf /var/lib/apt/lists/*
+
+############################################################ install ONTrack
+WORKDIR /home/tools/
+
+RUN git clone https://github.com/MaestSi/ONTrack.git
+WORKDIR /home/tools/ONTrack
+RUN chmod 755 *
+
+RUN sed -i 's/PIPELINE_DIR <- .*/PIPELINE_DIR <- \"\/home\/tools\/ONTrack\/\"/' config_MinION_mobile_lab.R
+RUN sed -i 's/MINICONDA_DIR <- .*/MINICONDA_DIR <- \"\/opt\/conda\/\"/' config_MinION_mobile_lab.R
+
+RUN conda config --add channels bioconda && \
+conda config --add channels anaconda && \
+conda config --add channels r && \
+conda config --add channels conda-forge
+RUN conda create -n ONTrack_env -c bioconda bioconductor-biostrings
+RUN conda install -n ONTrack_env python blast emboss vsearch seqtk mafft minimap2 samtools=1.15 nanopolish bedtools ncurses
+RUN /opt/conda/envs/ONTrack_env/bin/pip install pycoQC
+
+WORKDIR /home/