diff --git a/.github/dev-requirements.txt b/.github/dev-requirements.txt
index 0b29a8891..6116de386 100644
--- a/.github/dev-requirements.txt
+++ b/.github/dev-requirements.txt
@@ -1,4 +1,4 @@
 pre-commit
-black
+black==23.3.0
 isort
 flake8
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 414eb3704..038c25258 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -97,6 +97,8 @@ jobs:
         printf "\n\nmodule help ============================================\n"
         module help python/3.9.5-alpine
 
+        script_path=$(which python-exec)
+        cat $script_path
         set -x
         python-exec echo donuts >test_output
         cat test_output
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9b24f3334..b9c23ac4e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,7 @@ and **Merged pull requests**. Critical items to know are:
 The versions coincide with releases on pip. Only major versions will be released as tags on Github.
 
 ## [0.0.x](https://github.com/singularityhub/singularity-hpc/tree/main) (0.0.x)
+ - Allow custom location for wrapper scripts (0.1.24)
  - Labels with newlines need additional parsing (0.1.23)
  - Do not write directly to output with shpc show (0.1.22)
  - Podman template bug (0.1.21)
diff --git a/docs/getting_started/user-guide.rst b/docs/getting_started/user-guide.rst
index 9b935a54f..49cf8cd3c 100644
--- a/docs/getting_started/user-guide.rst
+++ b/docs/getting_started/user-guide.rst
@@ -176,6 +176,9 @@ variable replacement. A summary table of variables is included below, and then f
    * - module_base
      - The install directory for modules
      - $root_dir/modules
+   * - wrapper_base
+     - The install directory for script wrappers
+     - $root_dir/modules
    * - container_base
      - Where to install containers. If not defined, they are installed in "containers" in the install root
      - $root_dir/containers
@@ -347,6 +350,20 @@ Singularity Registry HPC uses this simple directory structure to ensure
 a unique namespace.
 
 
+Wrapper Base
+------------
+
+By default, if you do not set a wrapper script base they will be stored alongside
+modules. However, for large installations, we recommend you customize this path
+to be somewhere else. This way, you can avoid warnings from your module software
+about having too many files.
+
+.. code-block:: console
+
+    # an absolute path
+    $ shpc config set wrapper_base /opt/lmod/wrappers
+
+
 Container Images Folder
 -----------------------
 
diff --git a/shpc/main/container/base.py b/shpc/main/container/base.py
index afabadff0..f7d383886 100644
--- a/shpc/main/container/base.py
+++ b/shpc/main/container/base.py
@@ -66,13 +66,16 @@ def add(self, sif, module_name, modulefile, template, **kwargs):
         """
         logger.warning("Add is not supported for %s" % self)
 
-    def add_environment(self, module_dir, envars, environment_file):
+    def add_environment(self, env_dir, envars, environment_file):
         """
         Given one or more environment variables in a dictionary, write to file.
+
+        The environment file goes in the wrapper directory, which can default
+        to the module directory if the value uses the default or is unset.
         """
         # Podman envars are written directly to the module file
         out = Template(shpc.main.templates.environment_file).render(envars=envars)
-        env_file = os.path.join(module_dir, environment_file)
+        env_file = os.path.join(env_dir, environment_file)
         shpc.utils.write_file(env_file, out)
 
     def delete(self, image):
diff --git a/shpc/main/container/docker.py b/shpc/main/container/docker.py
index 7130b5d33..a55fc1bfb 100644
--- a/shpc/main/container/docker.py
+++ b/shpc/main/container/docker.py
@@ -218,7 +218,7 @@ def install(self, module_path, template, module, features=None):
         if self.settings.wrapper_scripts["enabled"] is True:
             wrapper_scripts = shpc.main.wrappers.generate(
                 aliases=aliases,
-                module_dir=module.module_dir,
+                wrapper_dir=module.wrapper_dir,
                 features=features,
                 container=self,
                 image=module.container_path,
diff --git a/shpc/main/container/singularity.py b/shpc/main/container/singularity.py
index 46fb60adb..1d5a5d428 100644
--- a/shpc/main/container/singularity.py
+++ b/shpc/main/container/singularity.py
@@ -211,9 +211,9 @@ def install(self, module_path, template, module, features=None):
         if self.settings.wrapper_scripts["enabled"] is True:
             wrapper_scripts = shpc.main.wrappers.generate(
                 aliases=aliases,
-                module_dir=module.module_dir,
                 features=features,
                 container=self,
+                wrapper_dir=module.wrapper_dir,
                 image=module.container_path,
                 config=module.config,
             )
diff --git a/shpc/main/container/update/versions.py b/shpc/main/container/update/versions.py
index 20e69dba7..39ac93097 100644
--- a/shpc/main/container/update/versions.py
+++ b/shpc/main/container/update/versions.py
@@ -155,7 +155,7 @@ def _cmp(self, other):
             this_version = self.version[i]
             other_version = other.version[i]
 
-            if type(this_version) != type(other_version):
+            if type(this_version) is not type(other_version):
                 continue
 
             if this_version == other_version:
diff --git a/shpc/main/modules/base.py b/shpc/main/modules/base.py
index 8b0058c0d..52908c380 100644
--- a/shpc/main/modules/base.py
+++ b/shpc/main/modules/base.py
@@ -130,6 +130,14 @@ def uninstall(self, name, force=False):
                 "$module_base/%s" % module.name,
             )
 
+        # If we have a wrapper
+        if module.wrapper_dir != module.module_dir:
+            self._uninstall(
+                module.wrapper_dir,
+                self.settings.wrapper_base,
+                "$wrapper_base/%s" % module.name,
+            )
+
         # If uninstalling the entire module, clean up symbolic links in all views
         for view_name in views_with_module:
             self.views[view_name].uninstall(module.module_dir)
diff --git a/shpc/main/modules/module.py b/shpc/main/modules/module.py
index d95bf9a17..1a16b671b 100644
--- a/shpc/main/modules/module.py
+++ b/shpc/main/modules/module.py
@@ -36,7 +36,7 @@ def add_environment(self):
         Write the environment to the module directory.
         """
         self.container.add_environment(
-            self.module_dir,
+            self.wrapper_dir,
             envars=self.config.get_envars(),
             environment_file=self.settings.environment_file,
         )
@@ -165,6 +165,14 @@ def uri(self):
         """
         return self._uri
 
+    @property
+    def wrapper_dir(self):
+        """
+        Full path to the wrapper directory
+        """
+        wrapper_dir = self.settings.wrapper_base or self.settings.module_base
+        return os.path.join(wrapper_dir, self.module_basepath)
+
     @property
     def module_dir(self):
         """
diff --git a/shpc/main/modules/templates/docker.lua b/shpc/main/modules/templates/docker.lua
index 575cb6347..845ac1bf9 100644
--- a/shpc/main/modules/templates/docker.lua
+++ b/shpc/main/modules/templates/docker.lua
@@ -16,18 +16,18 @@ Container:
 Commands include:
 
  - {|module_name|}-run:
-       {{ command }} run -i{% if settings.enable_tty %}t{% endif %} -u `id -u`:`id -g` --rm {% if settings.environment_file %}--env-file <moduleDir>/{{ settings.environment_file }} {% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %}-v ${PWD} -w ${PWD} <container> "$@"
+       {{ command }} run -i{% if settings.enable_tty %}t{% endif %} -u `id -u`:`id -g` --rm {% if settings.environment_file %}--env-file <wrapperDir>/{{ settings.environment_file }} {% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %}-v ${PWD} -w ${PWD} <container> "$@"
  - {|module_name|}-shell:
-       {{ command }} run -i{% if settings.enable_tty %}t{% endif %} -u `id -u`:`id -g` --rm {% if settings.environment_file %}--env-file <moduleDir>/{{ settings.environment_file }} {% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %}--entrypoint {{ shell }} -v ${PWD} -w ${PWD}<container>
+       {{ command }} run -i{% if settings.enable_tty %}t{% endif %} -u `id -u`:`id -g` --rm {% if settings.environment_file %}--env-file <wrapperDir>/{{ settings.environment_file }} {% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %}--entrypoint {{ shell }} -v ${PWD} -w ${PWD}<container>
  - {|module_name|}-exec:
-       {{ command }} run -i{% if settings.enable_tty %}t{% endif %} -u `id -u`:`id -g` --rm --entrypoint "" {% if settings.environment_file %}--env-file <moduleDir>/{{ settings.environment_file }} {% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %} -v ${PWD} -w ${PWD} <container> "$@"
+       {{ command }} run -i{% if settings.enable_tty %}t{% endif %} -u `id -u`:`id -g` --rm --entrypoint "" {% if settings.environment_file %}--env-file <wrapperDir>/{{ settings.environment_file }} {% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %} -v ${PWD} -w ${PWD} <container> "$@"
  - {|module_name|}-inspect:
        {{ command }} inspect <container>
  - {|module_name|}-container:
        echo "$PODMAN_CONTAINER"
 
 {% if aliases %}{% for alias in aliases %} - {{ alias.name }}:
-       {{ command }} run -i{% if settings.enable_tty %}t{% endif %} -u `id -u`:`id -g` --rm --entrypoint {{ alias.entrypoint }} {% if settings.environment_file %}--env-file <moduleDir>/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %}{% if alias.docker_options %}{{ alias.docker_options }} {% endif %} -v ${PWD} -w ${PWD} <container> "{{ alias.args }}" "$@"
+       {{ command }} run -i{% if settings.enable_tty %}t{% endif %} -u `id -u`:`id -g` --rm --entrypoint {{ alias.entrypoint }} {% if settings.environment_file %}--env-file <wrapperDir>/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %}{% if alias.docker_options %}{{ alias.docker_options }} {% endif %} -v ${PWD} -w ${PWD} <container> "{{ alias.args }}" "$@"
 {% endfor %}{% endif %}
 
 For each of the above, you can export:
@@ -48,23 +48,26 @@ if not os.getenv("PODMAN_COMMAND_OPTS") then setenv ("PODMAN_COMMAND_OPTS", "")
 -- directory containing this modulefile, once symlinks resolved (dynamically defined)
 local moduleDir = subprocess("realpath " .. myFileName()):match("(.*[/])") or "."
 
+-- If we have wrapper base set, honor it, otherwise we use the moduleDir
+{% if settings.wrapper_base %}local wrapperDir = "{{ module.wrapper_dir }}"{% else %}local wrapperDir = moduleDir{% endif %}
+
 -- interactive shell to any container, plus exec for aliases
 local containerPath = '{{ module.container_path }}'
 
 -- service environment variable to access docker URI
 setenv("PODMAN_CONTAINER", containerPath)
 
-local shellCmd = "{{ command }} ${PODMAN_OPTS} run -i{% if settings.enable_tty %}t{% endif %} ${PODMAN_COMMAND_OPTS} -u `id -u`:`id -g` --rm --entrypoint {{ shell }} {% if settings.environment_file %}--env-file " .. moduleDir .. "/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %} -v ${PWD} -w ${PWD} " .. containerPath
+local shellCmd = "{{ command }} ${PODMAN_OPTS} run -i{% if settings.enable_tty %}t{% endif %} ${PODMAN_COMMAND_OPTS} -u `id -u`:`id -g` --rm --entrypoint {{ shell }} {% if settings.environment_file %}--env-file " .. wrapperDir .. "/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %} -v ${PWD} -w ${PWD} " .. containerPath
 -- execCmd needs entrypoint to be the executor
-local execCmd = "{{ command }} ${PODMAN_OPTS} run ${PODMAN_COMMAND_OPTS} -i{% if settings.enable_tty %}t{% endif %} -u `id -u`:`id -g` --rm {% if settings.environment_file %}--env-file " .. moduleDir .. "/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %} -v ${PWD} -w ${PWD} "
-local runCmd = "{{ command }} ${PODMAN_OPTS} run ${PODMAN_COMMAND_OPTS} -i{% if settings.enable_tty %}t{% endif %} -u `id -u`:`id -g` --rm {% if settings.environment_file %}--env-file " .. moduleDir .. "/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %} -v ${PWD} -w ${PWD} " .. containerPath
+local execCmd = "{{ command }} ${PODMAN_OPTS} run ${PODMAN_COMMAND_OPTS} -i{% if settings.enable_tty %}t{% endif %} -u `id -u`:`id -g` --rm {% if settings.environment_file %}--env-file " .. wrapperDir .. "/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %} -v ${PWD} -w ${PWD} "
+local runCmd = "{{ command }} ${PODMAN_OPTS} run ${PODMAN_COMMAND_OPTS} -i{% if settings.enable_tty %}t{% endif %} -u `id -u`:`id -g` --rm {% if settings.environment_file %}--env-file " .. wrapperDir .. "/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %} -v ${PWD} -w ${PWD} " .. containerPath
 local inspectCmd = "{{ command }} ${PODMAN_OPTS} inspect ${PODMAN_COMMAND_OPTS} " .. containerPath
 
 -- conflict with modules with the same name
 conflict("{{ parsed_name.tool }}"{% if name != parsed_name.tool %},"{{ module.name }}"{% endif %}{% if aliases %}{% for alias in aliases %}{% if alias.name != parsed_name.tool %},"{{ alias.name }}"{% endif %}{% endfor %}{% endif %})
 
 -- if we have any wrapper scripts, add the bin directory
-{% if wrapper_scripts %}prepend_path("PATH", pathJoin(moduleDir, "bin")){% endif %}
+{% if wrapper_scripts %}prepend_path("PATH", pathJoin(wrapperDir, "bin")){% endif %}
 
 -- "aliases" to module commands - generate only if not a wrapper script already generated
 {% if aliases %}{% for alias in aliases %}{% if alias.name not in wrapper_scripts %}set_shell_function("{{ alias.name }}", execCmd .. {% if alias.docker_options %} "{{ alias.docker_options }} " .. {% endif %} " --entrypoint {{ alias.entrypoint }} " .. containerPath .. " {{ alias.args }} \"$@\"", execCmd .. {% if alias.docker_options %} "{{ alias.docker_options }} " .. {% endif %} " --entrypoint {{ alias.entrypoint }} " .. containerPath .. " {{ alias.args }}"){% endif %}
diff --git a/shpc/main/modules/templates/docker.tcl b/shpc/main/modules/templates/docker.tcl
index d8f1e663b..531d801b6 100644
--- a/shpc/main/modules/templates/docker.tcl
+++ b/shpc/main/modules/templates/docker.tcl
@@ -15,18 +15,18 @@ proc ModulesHelp { } {
     puts stderr " - {{ module.container_path }}"
     puts stderr "Commands include:"
     puts stderr " - {|module_name|}-run:"
-    puts stderr "       {{ command }} run -i{% if settings.enable_tty %}t{% endif %} -u `id -u`:`id -g` --rm {% if settings.environment_file %}--env-file  <moduleDir>/{{ settings.environment_file }} {% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %} -v . -w . <container> \"\$@\""
+    puts stderr "       {{ command }} run -i{% if settings.enable_tty %}t{% endif %} -u `id -u`:`id -g` --rm {% if settings.environment_file %}--env-file  <wrapperDir>/{{ settings.environment_file }} {% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %} -v . -w . <container> \"\$@\""
     puts stderr " - {|module_name|}-shell:"
-    puts stderr "       {{ command }} run -i{% if settings.enable_tty %}t{% endif %} -u `id -u`:`id -g` --rm --entrypoint {{ shell }} {% if settings.environment_file %} --env-file <moduleDir>/{{ settings.environment_file }} {% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %} -v . -w . <container>"
+    puts stderr "       {{ command }} run -i{% if settings.enable_tty %}t{% endif %} -u `id -u`:`id -g` --rm --entrypoint {{ shell }} {% if settings.environment_file %} --env-file <wrapperDir>/{{ settings.environment_file }} {% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %} -v . -w . <container>"
     puts stderr " - {|module_name|}-exec:"
-    puts stderr "       {{ command }} run -i{% if settings.enable_tty %}t{% endif %} -u `id -u`:`id -g` --rm --entrypoint \"\" {% if settings.environment_file %} --env-file  <moduleDir>/{{ settings.environment_file }} {% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %} -v . -w . <container> \"\$@\""
+    puts stderr "       {{ command }} run -i{% if settings.enable_tty %}t{% endif %} -u `id -u`:`id -g` --rm --entrypoint \"\" {% if settings.environment_file %} --env-file  <wrapperDir>/{{ settings.environment_file }} {% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %} -v . -w . <container> \"\$@\""
     puts stderr " - {|module_name|}-inspect:"
     puts stderr "       {{ command }} inspect <container>"
     puts stderr " - {|module_name|}-container:"
     puts stderr "       echo \"\$PODMAN_CONTAINER\""
     puts stderr ""
 {% if aliases %}{% for alias in aliases %}    puts stderr " - {{ alias.name }}:"
-    puts stderr "       {{ command }} run -i{% if settings.enable_tty %}t{% endif %} --rm -u `id -u`:`id -g` --entrypoint {{ alias.entrypoint | replace("$", "\$") }} {% if settings.environment_file %}--settings.environment_file  <moduleDir>/{{ settings.environment_file }} {% endif %}{% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %}{% if alias.docker_options %}{{ alias.docker_options | replace("$", "\$") }} {% endif %} -v . -w . <container> {{ alias.args | replace("$", "\$") }} \"\$@\""
+    puts stderr "       {{ command }} run -i{% if settings.enable_tty %}t{% endif %} --rm -u `id -u`:`id -g` --entrypoint {{ alias.entrypoint | replace("$", "\$") }} {% if settings.environment_file %}--settings.environment_file  <wrapperDir>/{{ settings.environment_file }} {% endif %}{% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %}{% if alias.docker_options %}{{ alias.docker_options | replace("$", "\$") }} {% endif %} -v . -w . <container> {{ alias.args | replace("$", "\$") }} \"\$@\""
 {% endfor %}{% endif %}
     puts stderr ""
     puts stderr "For each of the above, you can export:"
@@ -62,6 +62,9 @@ set helpcommand "This module is a {{ docker }} container wrapper for {{ module.n
 # directory containing this modulefile, once symlinks resolved (dynamically defined)
 set moduleDir   [file dirname [expr { [string equal [file type ${ModulesCurrentModulefile}] "link"] ? [file readlink ${ModulesCurrentModulefile}] : ${ModulesCurrentModulefile} }]]
 
+# If we have wrapper base set, honor it, otherwise we use the moduleDir
+{% if settings.wrapper_base %}set wrapperDir "{{ module.wrapper_dir }}"{% else %}set wrapperDir "${moduleDir}"{% endif %}
+
 # conflict with modules with the same alias name
 conflict {{ parsed_name.tool }}
 {% if name != parsed_name.tool %}conflict {{ module.name }}{% endif %}
@@ -72,15 +75,15 @@ conflict {{ parsed_name.tool }}
 setenv PODMAN_CONTAINER "${containerPath}"
 
 # interactive shell to any container, plus exec for aliases
-set shellCmd "{{ command }} \${PODMAN_OPTS} run \${PODMAN_COMMAND_OPTS} -u `id -u`:`id -g` --rm -i{% if settings.enable_tty %}t{% endif %} --entrypoint {{ shell }} {% if settings.environment_file %}--env-file ${moduleDir}/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %} -v $workdir -w $workdir ${containerPath}"
+set shellCmd "{{ command }} \${PODMAN_OPTS} run \${PODMAN_COMMAND_OPTS} -u `id -u`:`id -g` --rm -i{% if settings.enable_tty %}t{% endif %} --entrypoint {{ shell }} {% if settings.environment_file %}--env-file ${wrapperDir}/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %} -v $workdir -w $workdir ${containerPath}"
 
 # execCmd needs entrypoint to be the executor
-set execCmd "{{ command }} \${PODMAN_OPTS} run -i{% if settings.enable_tty %}t{% endif %} \${PODMAN_COMMAND_OPTS} -u `id -u`:`id -g` --rm {% if settings.environment_file %} --env-file ${moduleDir}/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }}{% endif %}{% if features.home %}-v {{ features.home }} {% endif %} -v $workdir -w $workdir"
-set runCmd "{{ command }} \${PODMAN_OPTS} run -i{% if settings.enable_tty %}t{% endif %} \${PODMAN_COMMAND_OPTS} -u `id -u`:`id -g` --rm {% if settings.environment_file %}--env-file  ${moduleDir}/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %} -v $workdir -w $workdir ${containerPath}"
+set execCmd "{{ command }} \${PODMAN_OPTS} run -i{% if settings.enable_tty %}t{% endif %} \${PODMAN_COMMAND_OPTS} -u `id -u`:`id -g` --rm {% if settings.environment_file %} --env-file ${wrapperDir}/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }}{% endif %}{% if features.home %}-v {{ features.home }} {% endif %} -v $workdir -w $workdir"
+set runCmd "{{ command }} \${PODMAN_OPTS} run -i{% if settings.enable_tty %}t{% endif %} \${PODMAN_COMMAND_OPTS} -u `id -u`:`id -g` --rm {% if settings.environment_file %}--env-file  ${wrapperDir}/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %} -v $workdir -w $workdir ${containerPath}"
 set inspectCmd "{{ command }} \${PODMAN_OPTS} inspect ${containerPath}"
 
 # wrapper scripts? Add bin to path
-{% if wrapper_scripts %}prepend-path PATH "${moduleDir}/bin"{% endif %}
+{% if wrapper_scripts %}prepend-path PATH ${wrapperDir}/bin{% endif %}
 
 # "aliases" to module commands
 {% if aliases %}if { [ module-info shell bash ] } {
diff --git a/shpc/main/modules/templates/singularity.lua b/shpc/main/modules/templates/singularity.lua
index 97ec76395..ccade2938 100644
--- a/shpc/main/modules/templates/singularity.lua
+++ b/shpc/main/modules/templates/singularity.lua
@@ -16,11 +16,11 @@ Container (available through variable SINGULARITY_CONTAINER):
 Commands include:
 
  - {|module_name|}-run:
-       singularity run {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if settings.environment_file %}-B <moduleDir>/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }} {% endif %}<container> "$@"
+       singularity run {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if settings.environment_file %}-B <wrapperDir>/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }} {% endif %}<container> "$@"
  - {|module_name|}-shell:
-       singularity shell -s {{ settings.singularity_shell }} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if settings.environment_file %}-B <moduleDir>/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }} {% endif %}<container>
+       singularity shell -s {{ settings.singularity_shell }} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if settings.environment_file %}-B <wrapperDir>/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }} {% endif %}<container>
  - {|module_name|}-exec:
-       singularity exec {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if settings.environment_file %}-B <moduleDir>/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }} {% endif %}<container> "$@"
+       singularity exec {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if settings.environment_file %}-B <wrapperDir>/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }} {% endif %}<container> "$@"
  - {|module_name|}-inspect-runscript:
        singularity inspect -r <container>
  - {|module_name|}-inspect-deffile:
@@ -29,7 +29,7 @@ Commands include:
        echo "$SINGULARITY_CONTAINER"
 
 {% if aliases %}{% for alias in aliases %} - {{ alias.name }}:
-       singularity exec {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if settings.environment_file %}-B <moduleDir>/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }} {% endif %}{% if alias.singularity_options %}{{ alias.singularity_options }} {% endif %}<container> {{ alias.command }} "$@"
+       singularity exec {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if settings.environment_file %}-B <wrapperDir>/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }} {% endif %}{% if alias.singularity_options %}{{ alias.singularity_options }} {% endif %}<container> {{ alias.command }} "$@"
 {% endfor %}{% endif %}
 
 For each of the above, you can export:
@@ -46,6 +46,9 @@ For each of the above, you can export:
 -- directory containing this modulefile, once symlinks resolved (dynamically defined)
 local moduleDir = subprocess("realpath " .. myFileName()):match("(.*[/])") or "."
 
+-- If we have wrapper base set, honor it, otherwise we use the moduleDir
+{% if settings.wrapper_base %}local wrapperDir = "{{ module.wrapper_dir }}"{% else %}local wrapperDir = moduleDir{% endif %}
+
 -- singularity environment variable to set shell
 setenv("SINGULARITY_SHELL", "{{ settings.singularity_shell }}")
 
@@ -58,16 +61,16 @@ local containerPath = '{{ module.container_path }}'
 setenv("SINGULARITY_CONTAINER", containerPath)
 
 -- interactive shell to any container, plus exec for aliases
-local shellCmd = "singularity ${SINGULARITY_OPTS} shell ${SINGULARITY_COMMAND_OPTS} -s {{ settings.singularity_shell }} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if settings.environment_file %}-B " .. moduleDir .. "/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }}{% endif %} " .. containerPath
-local execCmd = "singularity ${SINGULARITY_OPTS} exec ${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if settings.environment_file %}-B " .. moduleDir .. "/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }}{% endif %} "
-local runCmd = "singularity ${SINGULARITY_OPTS} run ${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if settings.environment_file %}-B " .. moduleDir .. "/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }}{% endif %} " .. containerPath
+local shellCmd = "singularity ${SINGULARITY_OPTS} shell ${SINGULARITY_COMMAND_OPTS} -s {{ settings.singularity_shell }} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if settings.environment_file %}-B " .. wrapperDir .. "/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }}{% endif %} " .. containerPath
+local execCmd = "singularity ${SINGULARITY_OPTS} exec ${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if settings.environment_file %}-B " .. wrapperDir .. "/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }}{% endif %} "
+local runCmd = "singularity ${SINGULARITY_OPTS} run ${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if settings.environment_file %}-B " .. wrapperDir .. "/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }}{% endif %} " .. containerPath
 local inspectCmd = "singularity ${SINGULARITY_OPTS} inspect ${SINGULARITY_COMMAND_OPTS} "
 
 -- conflict with modules with the same name
 conflict("{{ parsed_name.tool }}"{% if name != parsed_name.tool %},"{{ module.name }}"{% endif %}{% if aliases %}{% for alias in aliases %}{% if alias.name != parsed_name.tool %},"{{ alias.name }}"{% endif %}{% endfor %}{% endif %})
 
 -- if we have any wrapper scripts, add bin to path
-{% if wrapper_scripts %}prepend_path("PATH", pathJoin(moduleDir, "bin")){% endif %}
+{% if wrapper_scripts %}prepend_path("PATH", pathJoin(wrapperDir, "bin")){% endif %}
 
 -- "aliases" to module commands
 {% if aliases %}{% for alias in aliases %}{% if alias.name not in wrapper_scripts %}set_shell_function("{{ alias.name }}", execCmd .. {% if alias.singularity_options %} "{{ alias.singularity_options }} " .. {% endif %} containerPath .. " {{ alias.command }} \"$@\"", execCmd .. {% if alias.singularity_options %} "{{ alias.singularity_options }} " .. {% endif %} containerPath .. " {{ alias.command }}"){% endif %}
diff --git a/shpc/main/modules/templates/singularity.tcl b/shpc/main/modules/templates/singularity.tcl
index bcf45ac07..f21ccb3ad 100644
--- a/shpc/main/modules/templates/singularity.tcl
+++ b/shpc/main/modules/templates/singularity.tcl
@@ -67,6 +67,9 @@ set helpcommand "This module is a singularity container wrapper for {{ module.na
 # directory containing this modulefile, once symlinks resolved (dynamically defined)
 set moduleDir   [file dirname [expr { [string equal [file type ${ModulesCurrentModulefile}] "link"] ? [file readlink ${ModulesCurrentModulefile}] : ${ModulesCurrentModulefile} }]]
 
+# If we have wrapper base set, honor it, otherwise we use the moduleDir
+{% if settings.wrapper_base %}set wrapperDir "{{ module.wrapper_dir }}"{% else %}set wrapperDir "${moduleDir}"{% endif %}
+
 # conflict with modules with the same alias name
 conflict {{ parsed_name.tool }}
 {% if name != parsed_name.tool %}conflict {{ module.name }}{% endif %}
@@ -80,13 +83,13 @@ setenv SINGULARITY_SHELL {{ settings.singularity_shell }}
 setenv SINGULARITY_CONTAINER "${containerPath}"
 
 # interactive shell to any container, plus exec for aliases
-set shellCmd "singularity \${SINGULARITY_OPTS} shell \${SINGULARITY_COMMAND_OPTS} -s {{ settings.singularity_shell }} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home | replace("$", "\$") }} --home {{ features.home | replace("$", "\$") }} {% endif %}{% if features.x11 %}-B {{ features.x11 | replace("$", "\$") }} {% endif %}{% if settings.environment_file %}-B ${moduleDir}/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }}{% endif %} ${containerPath}"
-set execCmd "singularity \${SINGULARITY_OPTS} exec \${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home | replace("$", "\$") }} --home {{ features.home | replace("$", "\$") }} {% endif %}{% if features.x11 %}-B {{ features.x11 | replace("$", "\$") }} {% endif %}{% if settings.environment_file %}-B ${moduleDir}/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }}{% endif %} "
-set runCmd "singularity \${SINGULARITY_OPTS} run \${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home | replace("$", "\$") }} --home {{ features.home | replace("$", "\$") }} {% endif %}{% if features.x11 %}-B {{ features.x11 | replace("$", "\$") }} {% endif %}{% if settings.environment_file %}-B ${moduleDir}/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }}{% endif %} ${containerPath}"
+set shellCmd "singularity \${SINGULARITY_OPTS} shell \${SINGULARITY_COMMAND_OPTS} -s {{ settings.singularity_shell }} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home | replace("$", "\$") }} --home {{ features.home | replace("$", "\$") }} {% endif %}{% if features.x11 %}-B {{ features.x11 | replace("$", "\$") }} {% endif %}{% if settings.environment_file %}-B ${wrapperDir}/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }}{% endif %} ${containerPath}"
+set execCmd "singularity \${SINGULARITY_OPTS} exec \${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home | replace("$", "\$") }} --home {{ features.home | replace("$", "\$") }} {% endif %}{% if features.x11 %}-B {{ features.x11 | replace("$", "\$") }} {% endif %}{% if settings.environment_file %}-B ${wrapperDir}/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }}{% endif %} "
+set runCmd "singularity \${SINGULARITY_OPTS} run \${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home | replace("$", "\$") }} --home {{ features.home | replace("$", "\$") }} {% endif %}{% if features.x11 %}-B {{ features.x11 | replace("$", "\$") }} {% endif %}{% if settings.environment_file %}-B ${wrapperDir}/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }}{% endif %} ${containerPath}"
 set inspectCmd "singularity \${SINGULARITY_OPTS} inspect \${SINGULARITY_COMMAND_OPTS} "
 
 # if we have any wrapper scripts, add bin to path
-{% if wrapper_scripts %}prepend-path PATH "${moduleDir}/bin"{% endif %}
+{% if wrapper_scripts %}prepend-path PATH ${wrapperDir}/bin{% endif %}
 
 # "aliases" to module commands
 {% if aliases %}if { [ module-info shell bash ] } {
diff --git a/shpc/main/schemas.py b/shpc/main/schemas.py
index 1efdc2381..cc234550b 100644
--- a/shpc/main/schemas.py
+++ b/shpc/main/schemas.py
@@ -137,6 +137,7 @@
 settingsProperties = {
     "registry": {"type": "array", "items": {"type": "string"}},
     "sync_registry": {"type": "string"},
+    "wrapper_base": {"type": ["string", "null"]},
     "module_base": {"type": "string"},
     "container_base": {"type": ["string", "null"]},
     "namespace": {"type": ["string", "null"]},
diff --git a/shpc/main/wrappers/base.py b/shpc/main/wrappers/base.py
index fdf978468..98e1e0414 100644
--- a/shpc/main/wrappers/base.py
+++ b/shpc/main/wrappers/base.py
@@ -37,11 +37,13 @@ def container_dest_dir(self):
         return os.path.dirname(self.image)
 
     @property
-    def module_dir(self):
+    def wrapper_dir(self):
         """
-        Get the module directory (should error if not provided in kwargs)
+        Get the wrapper directory (should error if not provided in kwargs)
+
+        This can be the module directory or a custom wrapper directory.
         """
-        return self.kwargs["module_dir"]
+        return self.kwargs["wrapper_dir"]
 
     def get_template_paths(self):
         """
@@ -121,8 +123,8 @@ def generate(self, wrapper_name, alias_definition=None):
         interaction wrappers (e.g., exec, shell, etc.)
         """
 
-        # Write scripts into container directory
-        wrapper_dir = os.path.join(self.module_dir, "bin")
+        # Write scripts into custom module directory
+        wrapper_dir = os.path.join(self.wrapper_dir, "bin")
         shpc.utils.mkdirp([wrapper_dir])
         wrapper_path = os.path.join(wrapper_dir, wrapper_name)
 
@@ -132,7 +134,7 @@ def generate(self, wrapper_name, alias_definition=None):
             settings=self.settings,
             image=self.image,
             config=self.config,
-            # includes module_dir, features, etc
+            # includes wrapper_dir, features, etc
             **self.kwargs
         )
         shpc.utils.write_file(wrapper_path, out, exec=True)
diff --git a/shpc/main/wrappers/templates/bases/shell-script-base.sh b/shpc/main/wrappers/templates/bases/shell-script-base.sh
index 111f736c4..5d335656b 100755
--- a/shpc/main/wrappers/templates/bases/shell-script-base.sh
+++ b/shpc/main/wrappers/templates/bases/shell-script-base.sh
@@ -1,7 +1,6 @@
 #!{{ settings.wrapper_shell }}
 
 {% if '/csh' in settings.wrapper_shell %}set {% endif %}script=`realpath $0`
-{% if '/csh' in settings.wrapper_shell %}set {% endif %}wrapper_bin=`dirname $script`
-{% if '/csh' in settings.wrapper_shell %}set {% endif %}moduleDir=`dirname $wrapper_bin`
+{% if '/csh' in settings.wrapper_shell %}set {% endif %}wrapperDir=`dirname $script`/..
 
 {% block content %}{% endblock %}
diff --git a/shpc/main/wrappers/templates/docker.sh b/shpc/main/wrappers/templates/docker.sh
index eda8b65f1..2e92bd1df 100755
--- a/shpc/main/wrappers/templates/docker.sh
+++ b/shpc/main/wrappers/templates/docker.sh
@@ -1,4 +1,4 @@
 {% extends "bases/shell-script-base.sh" %}
 
-{% block content %}{{ container.command }} ${PODMAN_OPTS} run ${PODMAN_COMMAND_OPTS} -i{% if settings.enable_tty %}t{% endif %} -u `id -u`:`id -g` --rm {% if settings.environment_file %}--env-file $moduleDir/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %} -v ${PWD} -w ${PWD} {% if alias.docker_options %} {{ alias.docker_options }} {% endif %} --entrypoint {{ alias.entrypoint }} {{ image }} {{ alias.args }} {% if '/sh' in settings.wrapper_shell or '/bash' in settings.wrapper_shell %}"$@"{% elif '/csh' in settings.wrapper_shell %}$argv:q{% endif %}
+{% block content %}{{ container.command }} ${PODMAN_OPTS} run ${PODMAN_COMMAND_OPTS} -i{% if settings.enable_tty %}t{% endif %} -u `id -u`:`id -g` --rm {% if settings.environment_file %}--env-file $wrapperDir/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %} -v ${PWD} -w ${PWD} {% if alias.docker_options %} {{ alias.docker_options }} {% endif %} --entrypoint {{ alias.entrypoint }} {{ image }} {{ alias.args }} {% if '/sh' in settings.wrapper_shell or '/bash' in settings.wrapper_shell %}"$@"{% elif '/csh' in settings.wrapper_shell %}$argv:q{% endif %}
 {% endblock %}
diff --git a/shpc/main/wrappers/templates/docker/exec.sh b/shpc/main/wrappers/templates/docker/exec.sh
index 9de392494..b15194adb 100755
--- a/shpc/main/wrappers/templates/docker/exec.sh
+++ b/shpc/main/wrappers/templates/docker/exec.sh
@@ -1,4 +1,4 @@
 {% extends "bases/shell-script-base.sh" %}
 
-{% block content %}{{ container.command }} ${PODMAN_OPTS} run ${PODMAN_COMMAND_OPTS} -i{% if settings.enable_tty %}t{% endif %} -u `id -u`:`id -g` --rm {% if settings.environment_file %}--env-file $moduleDir/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %} -v ${PWD} -w ${PWD} {{ image }} {{ alias.args }} {% if '/sh' in settings.wrapper_shell or '/bash' in settings.wrapper_shell %}"$@"{% elif '/csh' in settings.wrapper_shell %}$argv:q{% endif %}
+{% block content %}{{ container.command }} ${PODMAN_OPTS} run ${PODMAN_COMMAND_OPTS} -i{% if settings.enable_tty %}t{% endif %} -u `id -u`:`id -g` --rm {% if settings.environment_file %}--env-file $wrapperDir/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %} -v ${PWD} -w ${PWD} {{ image }} {{ alias.args }} {% if '/sh' in settings.wrapper_shell or '/bash' in settings.wrapper_shell %}"$@"{% elif '/csh' in settings.wrapper_shell %}$argv:q{% endif %}
 {% endblock %}
diff --git a/shpc/main/wrappers/templates/docker/run.sh b/shpc/main/wrappers/templates/docker/run.sh
index 9de392494..b15194adb 100755
--- a/shpc/main/wrappers/templates/docker/run.sh
+++ b/shpc/main/wrappers/templates/docker/run.sh
@@ -1,4 +1,4 @@
 {% extends "bases/shell-script-base.sh" %}
 
-{% block content %}{{ container.command }} ${PODMAN_OPTS} run ${PODMAN_COMMAND_OPTS} -i{% if settings.enable_tty %}t{% endif %} -u `id -u`:`id -g` --rm {% if settings.environment_file %}--env-file $moduleDir/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %} -v ${PWD} -w ${PWD} {{ image }} {{ alias.args }} {% if '/sh' in settings.wrapper_shell or '/bash' in settings.wrapper_shell %}"$@"{% elif '/csh' in settings.wrapper_shell %}$argv:q{% endif %}
+{% block content %}{{ container.command }} ${PODMAN_OPTS} run ${PODMAN_COMMAND_OPTS} -i{% if settings.enable_tty %}t{% endif %} -u `id -u`:`id -g` --rm {% if settings.environment_file %}--env-file $wrapperDir/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %} -v ${PWD} -w ${PWD} {{ image }} {{ alias.args }} {% if '/sh' in settings.wrapper_shell or '/bash' in settings.wrapper_shell %}"$@"{% elif '/csh' in settings.wrapper_shell %}$argv:q{% endif %}
 {% endblock %}
diff --git a/shpc/main/wrappers/templates/docker/shell.sh b/shpc/main/wrappers/templates/docker/shell.sh
index 4081f6ff6..00e26d64e 100755
--- a/shpc/main/wrappers/templates/docker/shell.sh
+++ b/shpc/main/wrappers/templates/docker/shell.sh
@@ -1,4 +1,4 @@
 {% extends "bases/shell-script-base.sh" %}
 
-{% block content %}{{ container.command }} ${PODMAN_OPTS} run ${PODMAN_COMMAND_OPTS} -i{% if settings.enable_tty %}t{% endif %} -u `id -u`:`id -g` --rm {% if settings.environment_file %}--env-file $moduleDir/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %} -v ${PWD} -w ${PWD} --entrypoint {{ settings.wrapper_shell }} {{ image }} {% if '/sh' in settings.wrapper_shell or '/bash' in settings.wrapper_shell %}"$@"{% elif '/csh' in settings.wrapper_shell %}$argv:q{% endif %}
+{% block content %}{{ container.command }} ${PODMAN_OPTS} run ${PODMAN_COMMAND_OPTS} -i{% if settings.enable_tty %}t{% endif %} -u `id -u`:`id -g` --rm {% if settings.environment_file %}--env-file $wrapperDir/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-v {{ settings.bindpaths }} {% endif %}{% if features.home %}-v {{ features.home }} {% endif %} -v ${PWD} -w ${PWD} --entrypoint {{ settings.wrapper_shell }} {{ image }} {% if '/sh' in settings.wrapper_shell or '/bash' in settings.wrapper_shell %}"$@"{% elif '/csh' in settings.wrapper_shell %}$argv:q{% endif %}
 {% endblock %}
diff --git a/shpc/main/wrappers/templates/singularity.sh b/shpc/main/wrappers/templates/singularity.sh
index 98ab377c8..7c7f2aa3f 100755
--- a/shpc/main/wrappers/templates/singularity.sh
+++ b/shpc/main/wrappers/templates/singularity.sh
@@ -1,4 +1,4 @@
 {% extends "bases/shell-script-base.sh" %}
 
-{% block content %}singularity ${SINGULARITY_OPTS} exec ${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if settings.environment_file %}-B $moduleDir/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }}{% endif %} {% if alias.singularity_options %} {{ alias.singularity_options }} {% endif %} {{ image }} {{ alias.command }} {% if '/sh' in settings.wrapper_shell or '/bash' in settings.wrapper_shell %}"$@"{% elif '/csh' in settings.wrapper_shell %}$argv:q{% endif %}
+{% block content %}singularity ${SINGULARITY_OPTS} exec ${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if settings.environment_file %}-B $wrapperDir/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }}{% endif %} {% if alias.singularity_options %} {{ alias.singularity_options }} {% endif %} {{ image }} {{ alias.command }} {% if '/sh' in settings.wrapper_shell or '/bash' in settings.wrapper_shell %}"$@"{% elif '/csh' in settings.wrapper_shell %}$argv:q{% endif %}
 {% endblock %}
diff --git a/shpc/main/wrappers/templates/singularity/exec.sh b/shpc/main/wrappers/templates/singularity/exec.sh
index d2b70eaf1..3040e3c23 100644
--- a/shpc/main/wrappers/templates/singularity/exec.sh
+++ b/shpc/main/wrappers/templates/singularity/exec.sh
@@ -1,4 +1,4 @@
 {% extends "bases/shell-script-base.sh" %}
 
-{% block content %}singularity ${SINGULARITY_OPTS} exec ${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if settings.environment_file %}-B $moduleDir/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }}{% endif %} {% if alias.singularity_options %} {{ alias.singularity_options }} {% endif %} {{ image }} {% if '/sh' in settings.wrapper_shell or '/bash' in settings.wrapper_shell %}"$@"{% elif '/csh' in settings.wrapper_shell %}$argv:q{% endif %}
+{% block content %}singularity ${SINGULARITY_OPTS} exec ${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if settings.environment_file %}-B $wrapperDir/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }}{% endif %} {% if alias.singularity_options %} {{ alias.singularity_options }} {% endif %} {{ image }} {% if '/sh' in settings.wrapper_shell or '/bash' in settings.wrapper_shell %}"$@"{% elif '/csh' in settings.wrapper_shell %}$argv:q{% endif %}
 {% endblock %}
diff --git a/shpc/main/wrappers/templates/singularity/run.sh b/shpc/main/wrappers/templates/singularity/run.sh
index 5047be356..7da8a9da0 100644
--- a/shpc/main/wrappers/templates/singularity/run.sh
+++ b/shpc/main/wrappers/templates/singularity/run.sh
@@ -1,4 +1,4 @@
 {% extends "bases/shell-script-base.sh" %}
 
-{% block content %}singularity ${SINGULARITY_OPTS} run ${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if settings.environment_file %}-B $moduleDir/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }}{% endif %} {% if alias.singularity_options %} {{ alias.singularity_options }} {% endif %} {{ image }} {% if '/sh' in settings.wrapper_shell or '/bash' in settings.wrapper_shell %}"$@"{% elif '/csh' in settings.wrapper_shell %}$argv:q{% endif %}
+{% block content %}singularity ${SINGULARITY_OPTS} run ${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if settings.environment_file %}-B $wrapperDir/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }}{% endif %} {% if alias.singularity_options %} {{ alias.singularity_options }} {% endif %} {{ image }} {% if '/sh' in settings.wrapper_shell or '/bash' in settings.wrapper_shell %}"$@"{% elif '/csh' in settings.wrapper_shell %}$argv:q{% endif %}
 {% endblock %}
diff --git a/shpc/main/wrappers/templates/singularity/shell.sh b/shpc/main/wrappers/templates/singularity/shell.sh
index f1638686d..aac4116fa 100644
--- a/shpc/main/wrappers/templates/singularity/shell.sh
+++ b/shpc/main/wrappers/templates/singularity/shell.sh
@@ -1,4 +1,4 @@
 {% extends "bases/shell-script-base.sh" %}
 
-{% block content %}singularity ${SINGULARITY_OPTS} shell ${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if settings.environment_file %}-B $moduleDir/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }}{% endif %} -s {{ settings.wrapper_shell }} {{ image }}
+{% block content %}singularity ${SINGULARITY_OPTS} shell ${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if settings.environment_file %}-B $wrapperDir/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }}{% endif %} -s {{ settings.wrapper_shell }} {{ image }}
 {% endblock %}
diff --git a/shpc/settings.yml b/shpc/settings.yml
index e9d9f76eb..d74743824 100644
--- a/shpc/settings.yml
+++ b/shpc/settings.yml
@@ -45,6 +45,8 @@ container_base: $root_dir/containers
 # When parsing labels, replace newlines with this string
 label_separator: ', '
 
+wrapper_base: $root_dir/modules
+
 # Default root directory to create views
 views_base: $root_dir/views
 
diff --git a/shpc/tests/test_client.py b/shpc/tests/test_client.py
index b920d8db7..6cdfc85cf 100644
--- a/shpc/tests/test_client.py
+++ b/shpc/tests/test_client.py
@@ -44,10 +44,14 @@ def test_install_get(tmp_path, module_sys, module_file, container_tech, remote):
     assert os.path.exists(client.settings.module_base)
 
     module_dir = os.path.join(client.settings.module_base, "python", "3.9.2-alpine")
+    wrapper_dir = os.path.join(client.settings.wrapper_base, "python", "3.9.2-alpine")
+
     assert os.path.exists(module_dir)
     module_file = os.path.join(module_dir, module_file)
     assert os.path.exists(module_file)
-    env_file = os.path.join(module_dir, client.settings.environment_file)
+
+    # Environment file is in wrapper directory
+    env_file = os.path.join(wrapper_dir, client.settings.environment_file)
     assert os.path.exists(env_file)
 
     assert client.get("python:3.9.2-alpine")
diff --git a/shpc/tests/test_wrappers.py b/shpc/tests/test_wrappers.py
index 4fe6cecb3..0bb421fc0 100644
--- a/shpc/tests/test_wrappers.py
+++ b/shpc/tests/test_wrappers.py
@@ -13,6 +13,7 @@
 import shpc.main.container as container
 import shpc.main.registry as registry
 import shpc.main.wrappers.base as wrappers_base
+import shpc.utils as utils
 
 from .helpers import here, init_client
 
@@ -108,10 +109,13 @@ def test_wrapper_install(tmp_path, module_sys, module_file, container_tech):
     # Install known tag
     client.install("python:3.9.2-alpine")
     module_dir = os.path.join(client.settings.module_base, "python", "3.9.2-alpine")
+    wrapper_dir = os.path.join(client.settings.wrapper_base, "python", "3.9.2-alpine")
     assert os.path.exists(module_dir)
-    assert "bin" in os.listdir(module_dir)
-    module_bin = os.path.join(module_dir, "bin")
-    assert os.path.exists(module_bin)
+
+    # wrappers are installed to wrapper directory
+    assert "bin" in os.listdir(wrapper_dir)
+    wrapper_bin = os.path.join(wrapper_dir, "bin")
+    assert os.path.exists(wrapper_bin)
 
     requireds = [
         "python-container",
@@ -124,7 +128,7 @@ def test_wrapper_install(tmp_path, module_sys, module_file, container_tech):
         requireds += ["python-inspect-runscript", "python-inspect-deffile"]
     else:
         requireds += ["python-inspect"]
-    binaries = os.listdir(module_bin)
+    binaries = os.listdir(wrapper_bin)
     for required in requireds:
         assert required in binaries
 
@@ -154,6 +158,103 @@ def test_disabled_wrapper_install(tmp_path, module_sys, module_file, container_t
     assert "bin" not in os.listdir(module_dir)
 
 
+@pytest.mark.parametrize(
+    "module_sys,module_file,container_tech,wrapper_type",
+    [
+        ("lmod", "module.lua", "singularity", "custom"),
+        ("lmod", "module.lua", "singularity", "default"),
+        ("lmod", "module.lua", "singularity", "unset"),
+        ("lmod", "module.lua", "singularity", "disabled"),
+        ("lmod", "module.lua", "podman", "custom"),
+        ("lmod", "module.lua", "podman", "default"),
+        ("lmod", "module.lua", "podman", "unset"),
+        ("lmod", "module.lua", "podman", "disabled"),
+        ("tcl", "module.tcl", "singularity", "custom"),
+        ("tcl", "module.tcl", "singularity", "default"),
+        ("tcl", "module.tcl", "singularity", "unset"),
+        ("tcl", "module.tcl", "singularity", "disabled"),
+        ("tcl", "module.tcl", "podman", "custom"),
+        ("tcl", "module.tcl", "podman", "default"),
+        ("tcl", "module.tcl", "podman", "unset"),
+        ("tcl", "module.tcl", "podman", "disabled"),
+    ],
+)
+def test_custom_wrapper_dir(
+    tmp_path, module_sys, module_file, container_tech, wrapper_type
+):
+    """
+    Test that we can customize the install location of wrapper scripts
+
+    There are three cases:
+      - unset: the user explicitly sets to None
+      - default: we use the default value
+      - custom: we use a custom location
+    """
+
+    client = init_client(str(tmp_path), module_sys, container_tech)
+
+    if wrapper_type == "custom":
+        wrapper_dir = os.path.join(str(tmp_path), "wrappers")
+        client.settings.set("wrapper_base", wrapper_dir)
+
+    elif wrapper_type == "unset":
+        client.settings.set("wrapper_base", None)
+
+    # Note that if you set enabled to false but don't set path to None,
+    # we will still generate them, which likely is not desired
+    elif wrapper_type == "disabled":
+        client.settings.set("wrapper_scripts:enabled", False)
+        client.settings.set("wrapper_base", None)
+
+    # Default to $root/modules
+    elif wrapper_type == "default":
+        pass
+
+    # A custom wrapper directory should not have a bin in the module base
+    client.install("python:3.9.2-alpine")
+    module_dir = os.path.join(client.settings.module_base, "python", "3.9.2-alpine")
+    if client.settings.wrapper_base:
+        wrapper_dir = os.path.join(
+            client.settings.wrapper_base, "python", "3.9.2-alpine"
+        )
+    else:
+        wrapper_dir = module_dir
+
+    module_filepath = os.path.join(module_dir, module_file)
+
+    # Sanity check module is created and exists
+    assert os.path.exists(module_dir)
+    assert os.path.exists(module_filepath)
+
+    # The content of the file
+    content = utils.read_file(module_filepath)
+
+    print(module_file)
+    print(wrapper_type)
+
+    # For custom, wrapper_dir will have wrappers. For default, wrapper_dir will be modules
+    # directory. We can test the same way.
+    if module_file.endswith("lua") and wrapper_type in ["custom", "default"]:
+        assert f'local wrapperDir = "{wrapper_dir}"' in content
+
+    elif module_file.endswith("tcl") and wrapper_type in ["custom", "default"]:
+        assert f'set wrapperDir "{wrapper_dir}"' in content
+
+    elif module_file.endswith("lua") and wrapper_type in ["unset", "disabled"]:
+        assert "local wrapperDir = moduleDir" in content
+
+    elif module_file.endswith("tcl") and wrapper_type in ["unset", "disabled"]:
+        assert 'set wrapperDir "${moduleDir}"' in content
+
+    # Wrappers always generated in either wrapper_dir or module_dir, unless disabled
+    # bin is generated no matter what, but is populated in one case only
+    if wrapper_type == "disabled":
+        assert "bin" not in os.listdir(wrapper_dir)
+    else:
+        assert "bin" in os.listdir(wrapper_dir)
+        assert os.listdir(os.path.join(wrapper_dir, "bin"))
+
+
 @pytest.mark.parametrize(
     "make_absolute,exists",
     [
diff --git a/shpc/version.py b/shpc/version.py
index 311dbd49a..43fac3353 100644
--- a/shpc/version.py
+++ b/shpc/version.py
@@ -2,7 +2,7 @@
 __copyright__ = "Copyright 2021-2023, Vanessa Sochat"
 __license__ = "MPL 2.0"
 
-__version__ = "0.1.23"
+__version__ = "0.1.24"
 AUTHOR = "Vanessa Sochat"
 EMAIL = "vsoch@users.noreply.github.com"
 NAME = "singularity-hpc"