diff --git a/.github/scripts/configure.sh b/.github/scripts/configure.sh
new file mode 100755
index 00000000000..5cbeba245ad
--- /dev/null
+++ b/.github/scripts/configure.sh
@@ -0,0 +1,10 @@
+#!/bin/sh
+
+set -eu #Needed so CI fails when anything is wrong
+set -x
+
+#Any arguments are passed to configure
+
+cd src
+./autogen.sh
+./configure "$@" --disable-check-runtime-deps --enable-werror
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index c14721f6de8..0545a317a5e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -150,10 +150,13 @@ jobs:
     - name: Install dependencies
       run: |
         set -x
-        sudo apt-get -q update
+        .github/scripts/install-deps.sh
         sudo apt-get --yes install shellcheck
+    - name: Configure
+      run: |
+        set -x
+        .github/scripts/configure.sh
     - name: Shellcheck
-      continue-on-error: true
       run: |
         set -x
         scripts/shellcheck.sh
diff --git a/src/configure.ac b/src/configure.ac
index 15054b93100..86af93b5162 100644
--- a/src/configure.ac
+++ b/src/configure.ac
@@ -721,7 +721,7 @@ if test "xyes" = "x$RUN_IN_PLACE"; then
     EMC2_PO_DIR=$EMC2_HOME/share/locale
     EMC2_HELP_DIR=$EMC2_HOME/docs/help
     EMC2_RTLIB_DIR=$EMC2_HOME/rtlib
-    LINUXCNC_CONFIG_PATH="~/linuxcnc/configs:$EMC2_HOME/configs"
+    LINUXCNC_CONFIG_PATH="\$HOME/linuxcnc/configs:$EMC2_HOME/configs"
     LINUXCNC_CONFIG_PATH_TCL="$::env(HOME)/linuxcnc/configs:$EMC2_HOME/configs"
     EMC2_NCFILES_DIR=$EMC2_HOME/nc_files
     REALTIME=$EMC2_HOME/scripts/realtime
@@ -743,7 +743,7 @@ else
         */linuxcnc*) EMC2_RTLIB_DIR=$MODULE_DIR ;;
 	*) EMC2_RTLIB_DIR=$MODULE_DIR/linuxcnc
     esac
-    LINUXCNC_CONFIG_PATH="~/linuxcnc/configs:/usr/local/etc/linuxcnc/configs:"$(eval echo $EMC2_HELP_DIR)"/examples/sample-configs"
+    LINUXCNC_CONFIG_PATH="\$HOME/linuxcnc/configs:/usr/local/etc/linuxcnc/configs:"$(eval echo $EMC2_HELP_DIR)"/examples/sample-configs"
     LINUXCNC_CONFIG_PATH_TCL="$::env(HOME)/linuxcnc/configs:/usr/local/etc/linuxcnc/configs:"$(eval echo $EMC2_HELP_DIR)"/examples/sample-configs"
     EMC2_NCFILES_DIR=${prefix}/share/linuxcnc/ncfiles
     REALTIME=${prefix}/lib/linuxcnc/realtime