remove gosu

by moving from gosu to setpriv we remove one external dependency, while making the docker image smaller.
AlgoLab · Apr 8, 2021 · 0bf36cb · 0bf36cb
1 parent b751d3a
commit 0bf36cb
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Showing 2 changed files with 10 additions and 20 deletions.
diff --git a/docker/Dockerfile b/docker/Dockerfile
@@ -1,4 +1,4 @@
-FROM ubuntu:18.04
+FROM ubuntu:20.04
 
 ## for apt to be noninteractive
 ENV DEBIAN_FRONTEND noninteractive
@@ -27,22 +27,12 @@ RUN apt-get install -qqy \
     python3-pysam \
     python3-setuptools \
     samtools \
+    util-linux \
     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 --depth=1 --recursive https://github.com/AlgoLab/galig.git
 RUN cd galig ; make prerequisites
 RUN cd galig ; make

diff --git a/docker/asgal-docker.sh b/docker/asgal-docker.sh
@@ -6,7 +6,7 @@ USER_ID=$(/usr/bin/stat -c %u /data)
 GROUP_ID=$(/usr/bin/stat -c %g /data)
 
 # When running as root, use a dummy command to change user
-GOSU_CMD="gosu root:root"
+SU_CMD="setpriv --reuid=root --regid=root"
 
 # If the owner is not root, we create user:group with the correct uid:gid
 if [ "$USER_ID" != "0" ]
@@ -15,7 +15,7 @@ then
     groupadd -g "$GROUP_ID" group
     useradd --shell /bin/bash -u "$USER_ID" -g group -o -c "" -m user
     chown --recursive "$USER_ID":"$GROUP_ID" /data
-    GOSU_CMD="gosu user:group"
+    SU_CMD="setpriv --reuid=user --regid=group --init-groups"
 fi
 export HOME=/
 
@@ -27,7 +27,7 @@ then
     then
 	if [ -s /data/sample_2.fq ]
 	then
-	    $GOSU_CMD       \
+	    $SU_CMD       \
 		/galig/asgal --multi \
 		             -g /data/genome.fa \
 			     -a /data/annotation.gtf \
@@ -36,7 +36,7 @@ then
 			     -t /data/transcripts.fa \
 			     -o /data/output
 	else
-	    $GOSU_CMD       \
+	    $SU_CMD       \
 		/galig/asgal --multi \
 		             -g /data/genome.fa \
 			     -a /data/annotation.gtf \
@@ -47,7 +47,7 @@ then
     else
 	if [ -s /data/sample_2.fa ]
 	then
-	    $GOSU_CMD       \
+	    $SU_CMD       \
 		/galig/asgal --multi \
 		             -g /data/genome.fa \
 			     -a /data/annotation.gtf \
@@ -56,7 +56,7 @@ then
 			     -t /data/transcripts.fa \
 			     -o /data/output
 	else
-	    $GOSU_CMD       \
+	    $SU_CMD       \
 		/galig/asgal --multi \
 		             -g /data/genome.fa \
 			     -a /data/annotation.gtf \
@@ -68,13 +68,13 @@ then
 else
     if [ -s /data/sample_1.fq ]
     then
-	$GOSU_CMD       \
+	$SU_CMD       \
 	    /galig/asgal -g /data/genome.fa \
 	                 -a /data/annotation.gtf \
 			 -s /data/sample_1.fq \
 			 -o /data/output
     else
-	$GOSU_CMD       \
+	$SU_CMD       \
 	    /galig/asgal -g /data/genome.fa \
 	                 -a /data/annotation.gtf \
 			 -s /data/sample_1.fa \