Fix absolute paths in scripts

This removes some of the wrong paths pointing to the build location of the
AppImage by using a different shebang and some environment variables.

Fixes #12, #25 and #32

linuxdeploy-plugin-conda.sh

@@ -9,6 +9,7 @@ fi
 
 script=$(readlink -f "$0")
 
+CONDA_SKIP_ADJUST_PATHS=${CONDA_SKIP_ADJUST_PATHS:-"1"}
 ARCH="${ARCH:-"$(uname -m)"}"
 
 show_usage() {
@@ -23,6 +24,7 @@ show_usage() {
     echo "  PIP_REQUIREMENTS=\"packageA packageB -r requirements.txt -e git+https://...\""
     echo "  PIP_PREFIX=\"AppDir/usr/share/conda\""
     echo "  ARCH=\"$ARCH\" (supported values: x86_64, i368, i686)"
+    echo "  CONDA_SKIP_ADJUST_PATHS=\"1\" (default: skip)"
     echo "  CONDA_SKIP_CLEANUP=\"[all;][conda-pkgs;][__pycache__;][strip;][.a;][cmake;][doc;][man;][site-packages;]\""
 }
 
@@ -187,6 +189,41 @@ for i in usr/conda/bin/*; do
 done
 popd
 
+# adjust absolute paths, by default skipped via $CONDA_SKIP_ADJUST_PATHS
+if [ "$CONDA_SKIP_ADJUST_PATHS" != "1" ]; then
+    # disable history substitution, b/c we use ! in quoted strings
+    set +H
+    APPDIR_FULL="$(pwd)/$APPDIR"
+    # replace absolute paths in some scripts
+    sed -i "s|'$APPDIR_FULL|\"\${APPDIR}\"'|g" "$APPDIR"/usr/conda/etc/profile.d/conda.sh
+    sed -i "s|$APPDIR_FULL|\${APPDIR}|g" "$APPDIR"/usr/conda/etc/profile.d/conda.csh
+    sed -i "s|$APPDIR_FULL|\$APPDIR|g" "$APPDIR"/usr/conda/etc/fish/conf.d/conda.fish
+    sed -i "s|^#!$APPDIR_FULL/usr/conda/bin/|#!/usr/bin/env |" "$APPDIR"/usr/conda/condabin/conda
+    sed -i "s|$APPDIR_FULL|\${APPDIR}|g" "$APPDIR"/usr/bin/python3-config
+    sed -i "s|$APPDIR_FULL|\${APPDIR}|g" "$APPDIR"/usr/bin/python3.8-config
+    sed -i "s|$APPDIR_FULL|\${APPDIR}|g" "$APPDIR"/usr/bin/ncursesw6-config
+    # perl
+    sed -i "s|^#!$APPDIR_FULL/usr/conda/bin/|#!/usr/bin/env |" "$APPDIR"/usr/bin/c_rehash
+    sed -i "s|= \"$APPDIR_FULL|= \$ENV{APPDIR} . \"|g" "$APPDIR"/usr/bin/c_rehash
+    pushd "$APPDIR"
+    for i in usr/conda/bin/*; do
+        sed -i "s|^#!$APPDIR_FULL/usr/conda/bin/|#!/usr/bin/env |" "$i"
+        sed -i "s|=\"$APPDIR_FULL|=\"\${APPDIR}|g" "$i"
+    done
+    popd
+
+    # generate linuxdeploy-plugin-conda-hook
+    mkdir -p "$APPDIR"/apprun-hooks
+    cat > "$APPDIR"/apprun-hooks/linuxdeploy-plugin-conda-hook.sh <<\EOF
+# generated by linuxdeploy-plugin-conda
+
+# export APPDIR variable to allow for running from extracted AppDir as well
+export APPDIR=${APPDIR:-$(readlink -f $(dirname "$0"))}
+# export PATH to allow /usr/bin/env shebangs to use the supplied applications
+export PATH="$APPDIR"/usr/bin:"$PATH"
+EOF
+
+fi
 
 # remove bloat, optionally skipped via $CONDA_SKIP_CLEANUP
 IFS=';' read -ra cleanup <<< "$CONDA_SKIP_CLEANUP"