Merge pull request #68 from nmfs-opensci/dev

fix texlive and clean desktop

Desktop/README.md

@@ -0,0 +1 @@
+This is a folder Desktop apps files: .desktop, .xml, .png

appendix

@@ -6,8 +6,6 @@ ENV R_DOCKERFILE="verse_${R_VERSION}"
 RUN PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin && \
   chmod +x ${REPO_DIR}/rocker.sh && \
   ${REPO_DIR}/rocker.sh
-# Missing some basic tex packages
-RUN tlmgr install collection-latexrecommended && tlmgr clean --all
 
 # Install extra cmd line packages after R installation
 # The package_list part is reading the file and doing clean-up to just have the list of packages
@@ -28,5 +26,9 @@ RUN yes | unminimize
 ENV MANPATH="${NB_PYTHON_PREFIX}/share/man:${MANPATH}"
 RUN mandb
 
+# Copy Desktop files into ${REPO_DIR}/Desktop if they exist
+ONBUILD RUN mkdir -p ${REPO_DIR}/Desktop && \
+            if [ -d Desktop ]; then cp Desktop/* ${REPO_DIR}/Desktop/; fi
+
 # Revert to default user
 USER ${NB_USER}

rocker.sh

@@ -39,3 +39,9 @@ while IFS= read -r line; do
         eval "$cmd" # || echo ${cmd}" encountered an error, but continuing..."
     fi
 done < /rocker_scripts/original.Dockerfile
+
+# Install extra tex packages that are not installed by default
+if command -v tlmgr &> /dev/null; then
+    echo "Installing texlive collection-latexrecommended..."
+    tlmgr install collection-latexrecommended
+fi

start

@@ -19,9 +19,13 @@ shopt -s nullglob
 # build-time.
 APPLICATIONS_DIR="${HOME}/.local/share/applications"
 DESKTOP_DIR="${HOME}/Desktop"
+# Remove DESKTOP_DIR if it exists to avoid leftover files
+if [ -d "${DESKTOP_DIR}" ]; then
+    rm -rf "${DESKTOP_DIR}"
+fi
 mkdir -p "${APPLICATIONS_DIR}"
 mkdir -p "${DESKTOP_DIR}"
-for desktop_file_path in ${REPO_DIR}/*.desktop; do
+for desktop_file_path in ${REPO_DIR}/Desktop/*.desktop; do
     cp "${desktop_file_path}" "${APPLICATIONS_DIR}/."
 
     # Symlink application to desktop
@@ -30,11 +34,11 @@ for desktop_file_path in ${REPO_DIR}/*.desktop; do
 done
 update-desktop-database "${APPLICATIONS_DIR}"
 
-# Add MIME Type data from XML files in `mime/` dir to the MIME database.
+# Add MIME Type data from XML files  to the MIME database.
 MIME_DIR="${HOME}/.local/share/mime"
 MIME_PACKAGES_DIR="${MIME_DIR}/packages"
 mkdir -p "${MIME_PACKAGES_DIR}"
-for mime_file_path in ${REPO_DIR}/mime/*.xml; do
+for mime_file_path in ${REPO_DIR}/Desktop/*.xml; do
     cp "${mime_file_path}" "${MIME_PACKAGES_DIR}/."
 done
 update-mime-database "${MIME_DIR}"