Merge branch 'develop' of https://github.com/mskcc/vaporware into dev…

…elop

containers/facets-suite/Dockerfile

@@ -2,16 +2,16 @@ FROM frolvlad/alpine-glibc:alpine-3.9
 
 LABEL maintainer="Nikhil Kumar ([email protected])" \
       version.image="1.0.0" \
-      version.facets_suite="1.5.6" \
+      version.facets_suite="1.5.7" \
       version.facets="0.5.14"\
       version.alpine="3.8" \
       version.r="3.5.1" \
       version.pctGCdata="0.2.0" \
-      source.facets_suite="https://github.com/mskcc/facets-suite/releases/tag/1.5.6" \
+      source.facets_suite="https://github.com/mskcc/facets-suite/releases/tag/1.5.7" \
       source.facets="https://github.com/mskcc/facets/archive/v0.5.14.tar.gz"\
       source.r="https://pkgs.alpinelinux.org/package/edge/community/x86/R"
 
-ENV FACETS_SUITE_VERSION 1.5.6
+ENV FACETS_SUITE_VERSION 1.5.7
 ENV FACETS_VERSION 0.5.14
 ENV PCTGCDATA 0.2.0
 
@@ -24,6 +24,8 @@ RUN apk add --update \
         && apk add cairo cairo-dev libxt-dev libxml2-dev font-xfree86-type1 \
     # download and install R
         && apk add R R-dev \
+    # change permissions for /tmp; still doesn't resolve R warnings
+        && chmod  777 -R /tmp \
     # download and unzip facets, facets-suite, pctGCdata
         && cd /tmp \
 	    && wget https://github.com/mskcc/facets-suite/archive/${FACETS_SUITE_VERSION}.tar.gz -O facets-suite-${FACETS_SUITE_VERSION}.tar.gz \
@@ -53,7 +55,7 @@ RUN apk add --update \
                 && sed -i "s/opt\/common\/CentOS_6-dev\/R\/R-3.2.2\//usr\//g" *.R \
             # copy execs to /usr/bin/facets-suite
                 && mkdir -p /usr/bin/facets-suite/ \
-                && cp /tmp/facets-suite-${FACETS_SUITE_VERSION}/* /usr/bin/facets-suite/ \
+                && cp -r /tmp/facets-suite-${FACETS_SUITE_VERSION}/* /usr/bin/facets-suite/ \
     # clean up
         && rm -rf /var/cache/apk/* /tmp/*