From 472e2ab3c4aa810987091c97b103eb2383633844 Mon Sep 17 00:00:00 2001
From: Joshua Shapiro <josh.shapiro@ccdatalab.org>
Date: Fri, 3 Jan 2025 18:50:06 -0500
Subject: [PATCH] Install zellkonverter env as rstudio user

---
 analyses/cell-type-wilms-tumor-06/Dockerfile | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/analyses/cell-type-wilms-tumor-06/Dockerfile b/analyses/cell-type-wilms-tumor-06/Dockerfile
index 63134526d..7df1fc38e 100644
--- a/analyses/cell-type-wilms-tumor-06/Dockerfile
+++ b/analyses/cell-type-wilms-tumor-06/Dockerfile
@@ -30,8 +30,13 @@ RUN Rscript -e 'renv::restore()' && \
   rm -rf /tmp/downloaded_packages && \
   rm -rf /tmp/Rtmp*
 
-# Complete installation of zellkonverter conda env
-ENV BASILISK_EXTERNAL_DIR /usr/local/renv/basilisk
-RUN Rscript -e "proc <- basilisk::basiliskStart(env = zellkonverter::zellkonverterAnnDataEnv(), testload = 'anndata'); \
+# Set basilisk directory and set for rstudio user
+ENV BASILISK_EXTERNAL_DIR=/usr/share/basilisk
+RUN mkdir -p ${BASILISK_EXTERNAL_DIR} && \
+  chown rstudio:rstudio ${BASILISK_EXTERNAL_DIR}
+# install zellkonverter environment as rstudio user
+RUN sudo -u rstudio \
+  Rscript -e "Sys.setenv(BASILISK_EXTERNAL_DIR = '${BASILISK_EXTERNAL_DIR}'); \
+  proc <- basilisk::basiliskStart(env = zellkonverter::zellkonverterAnnDataEnv(), testload = 'anndata'); \
   basilisk::basiliskStop(proc); \
   basilisk.utils::cleanConda()"