Merge pull request #8 from AlgoLab/issue-#7

Issue #7

docker/Dockerfile

@@ -0,0 +1,53 @@
+FROM ubuntu:18.04
+
+## for apt to be noninteractive
+ENV DEBIAN_FRONTEND noninteractive
+ENV DEBCONF_NONINTERACTIVE_SEEN true
+
+RUN apt update -qqy
+RUN apt-get install -qqy apt-utils
+
+RUN echo 'tzdata tzdata/Areas select Etc' | debconf-set-selections; \
+    echo 'tzdata tzdata/Zones/Etc select UTC' | debconf-set-selections; \
+    apt-get install -qqy --no-install-recommends tzdata
+
+## preesed tzdata, update package index, upgrade packages and install needed software
+RUN apt-get install -qqy \
+    build-essential \
+    ca-certificates \
+    cmake \
+    dirmngr \
+    git \
+    make \
+    python3 \
+    python3-biopython \
+    python3-biopython-sql \
+    python3-pandas \
+    python3-pip \
+    python3-pysam \
+    python3-setuptools \
+    samtools \
+    wget \
+    zlib1g-dev
+RUN apt-get clean
+RUN pip3 install gffutils
+
+
+# Install gosu
+ENV GOSU_VERSION 1.12
+RUN set -eux; \
+	dpkgArch="$(dpkg --print-architecture | awk -F- '{ print $NF }')"; \
+	wget -O /usr/local/bin/gosu "https://github.com/tianon/gosu/releases/download/$GOSU_VERSION/gosu-$dpkgArch"; \
+	chmod +x /usr/local/bin/gosu; \
+# verify that the binary works
+	gosu --version; \
+	gosu nobody true
+
+RUN git clone --recursive https://github.com/AlgoLab/galig.git
+RUN cd galig ; make prerequisites
+RUN cd galig ; make
+
+VOLUME ["/data"]
+COPY asgal-docker.sh /galig/asgal-docker.sh
+ENV PATH=$PATH:/galig/asgal
+ENTRYPOINT ["/galig/asgal-docker.sh"]

asgal-docker.sh → docker/asgal-docker.sh

@@ -1,9 +1,22 @@
 #!/bin/bash
 
+# Add local user
+# with the same owner as /data
+USER_ID=$(stat -c %u /data)
+GROUP_ID=$(stat -c %g /data)
+
+echo "Starting with UID:GID $USER_ID:$GROUP_ID"
+# We create user:group with the correct uid:gid
+groupadd -g "$GROUP_ID" group
+useradd --shell /bin/bash -u "$USER_ID" -g group -o -c "" -m user
+export HOME=/
+chown --recursive "$USER_ID":"$GROUP_ID" /data
+
 if [ -s /data/transcripts.fa ]
 then
     if [ -s /data/sample_2.fa ]
     then
+    gosu user:group \
 	/galig/asgal --multi \
 		     -g /data/genome.fa \
 		     -a /data/annotation.gtf \
@@ -12,6 +25,7 @@ then
 		     -t /data/transcripts.fa \
 		     -o /data/output
     else
+    gosu user:group \
 	/galig/asgal --multi \
 		     -g /data/genome.fa \
 		     -a /data/annotation.gtf \
@@ -20,6 +34,7 @@ then
 		     -o /data/output
     fi
 else
+    gosu user:group \
     /galig/asgal -g /data/genome.fa \
 		 -a /data/annotation.gtf \
 		 -s /data/sample_1.fa \