explicitly export XML config as env

DataBiosphere · Sep 11, 2024 · 011afc4 · 011afc4
1 parent 1d61fdd
commit 011afc4
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/terra-jupyter-r/Dockerfile b/terra-jupyter-r/Dockerfile
@@ -117,8 +117,10 @@ RUN apt-get update \
 # Add libsbml CFLAGS
 ENV LIBSBML_CFLAGS="-I/usr/include"
 ENV LIBSBML_LIBS="-lsbml"
+ENV XML_CONFIG="/opt/conda/bin/xml2-config"
 RUN echo 'export LIBSBML_CFLAGS="-I/usr/include"' >> /etc/profile \
-    && echo 'export LIBSBML_LIBS="-lsbml"' >> /etc/profile
+    && echo 'export LIBSBML_LIBS="-lsbml"' >> /etc/profile \
+	&& echo 'export XML_CONFIG="/opt/conda/bin/xml2-config"' >> /etc/profile
 
 ## set pip3 to run as root, not as jupyter user
 ENV PIP_USER=false
@@ -168,7 +170,6 @@ RUN R -e 'install.packages("BiocManager")' \
 # Install Bioconductor packages found at:
 # https://raw.githubusercontent.com/anvilproject/anvil-docker/master/anvil-rstudio-bioconductor/install.R
 RUN R -e 'BiocManager::install(c( \
-	"XML", \
     "AnVIL", \
     "SingleCellExperiment", \
     "GenomicFeatures", \