From 620779605583f52b4bdd250dc14a3c49a02a5ec1 Mon Sep 17 00:00:00 2001
From: stevetsa <mylagimail2004@yahoo.com>
Date: Wed, 24 Jan 2018 17:11:26 -0500
Subject: [PATCH] add Dockerfile

---
 Dockerfile | 83 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 83 insertions(+)
 create mode 100644 Dockerfile

diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..47dbe4b
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,83 @@
+# Base Image
+FROM ncbihackathon/ncbihackathonbase:latest
+
+# Metadata
+LABEL base.image="ncbihackathonbase:latest"
+LABEL version="1"
+LABEL software="NCBI Hackathon Image for NGS analysis"
+LABEL software.version="0.0.1"
+LABEL description="NCBI Hackathons Image for NGS analysis"
+LABEL website="https://github.com/NCBI-Hackathons/HackathonDockerImages/Docker/ngs"
+LABEL documentation="https://github.com/NCBI-Hackathons/HackathonDockerImages/Docker/ngs"
+LABEL license="https://github.com/NCBI-Hackathons/HackathonDockerImages/LICENSE"
+LABEL tags="NCBI, Hackathon, Bioconductor"
+
+# Maintainer
+MAINTAINER Roberto Vera Alvarez <r78v10a07@gmail.com>
+
+USER biodocker
+
+RUN git clone --recursive https://github.com/NCBI-Hackathons/NanoporeMapper.git
+
+# Samtools 1.6
+ENV ZIP=samtools-1.6.tar.bz2
+ENV URL=https://github.com/samtools/samtools/releases/download/1.6/
+ENV FOLDER=samtools-1.6
+ENV DST=/tmp
+
+RUN wget $URL/$ZIP -O $DST/$ZIP && \
+    tar xvf $DST/$ZIP -C $DST && \
+    rm $DST/$ZIP && \
+    cd $DST/$FOLDER && \
+		./configure --prefix=/home/biodocker && \
+    make && \
+    make install && \
+    cd / && \
+    rm -rf $DST/$FOLDER
+
+# BAMTools 2.5.1
+ENV ZIP=v2.5.1.tar.gz
+ENV URL=https://github.com/pezmaster31/bamtools/archive/
+ENV FOLDER=bamtools-2.5.1
+ENV INSTALL_FOLDER=/home/biodocker/
+ENV DST=/tmp
+ENV LD_LIBRARY_PATH=$INSTALL_FOLDER/lib/bamtools:$LD_LIBRARY_PATH
+
+RUN cd $DST && \
+	wget $URL/$ZIP -O $DST/$ZIP && \
+	tar xzfv $DST/$ZIP -C $DST && \
+	cd $DST/$FOLDER && mkdir build && cd build && \
+	cmake -DCMAKE_INSTALL_PREFIX=$INSTALL_FOLDER .. && make && \
+	make install && \
+	rm -rf $DST/$FOLDER $DST/$ZIP
+
+# STAR 2.5.3a
+ENV ZIP=2.5.3a.tar.gz
+ENV URL=https://github.com/alexdobin/STAR/archive/
+ENV FOLDER=STAR-2.5.3a
+ENV INSTALL_FOLDER=/home/biodocker/
+ENV DST=/tmp
+
+RUN cd $DST && \
+	wget $URL/$ZIP -O $DST/$ZIP && \
+	tar xzfv $DST/$ZIP -C $DST && \
+	cd $DST/$FOLDER/source && \
+	make && \
+	mv STAR /home/biodocker/bin/ && \
+	rm -rf $DST/$FOLDER $DST/$ZIP
+
+# NCBI-magicblast 1.3.0
+ENV ZIP=ncbi-magicblast-1.3.0-x64-linux.tar.gz
+ENV URL=ftp://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/1.3.0/
+ENV FOLDER=ncbi-magicblast-1.3.0
+ENV INSTALL_FOLDER=/home/biodocker/
+ENV DST=/tmp
+
+RUN cd $DST && \
+	wget $URL/$ZIP -O $DST/$ZIP && \
+	tar xzfv $DST/$ZIP -C $DST && \
+	mv $DST/$FOLDER/LICENSE $DST/$FOLDER/README /home/biodocker/bin/ && \
+	mv $DST/$FOLDER/bin/* /home/biodocker/bin/ && \
+	rm -rf $DST/$FOLDER
+
+WORKDIR /data/