diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 0000000..6125df5
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1,7 @@
+.idea/
+target/
+.git/
+.gitignore
+.dockerignore
+Dockerfile
+examples/
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
new file mode 100644
index 0000000..ba2c16c
--- /dev/null
+++ b/.github/workflows/ci.yml
@@ -0,0 +1,92 @@
+name: build
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+  release:
+    types: [ created ]
+
+jobs:
+  build:
+    name: Build
+    runs-on: ubuntu-20.04
+
+    steps:
+      - name: Get git tag
+        id: git_info
+        if: startsWith(github.ref, 'refs/tags/')
+        run: echo "::set-output name=tag::${GITHUB_REF##*/}"
+      - name: Get project info
+        id: determine
+        env:
+          git_tag: ${{ steps.git_info.outputs.tag }}
+        run: |
+          repo="${GITHUB_REPOSITORY,,}"  # to lower case
+          # if build triggered by tag, use tag name
+          tag="${git_tag:-latest}"
+
+          # if tag is a version number prefixed by 'v', remove the 'v'
+          if [[ "$tag" =~ ^v[0-9].* ]]; then
+            tag="${tag:1}"
+          fi
+
+          dock_image=$repo:$tag
+          echo $dock_image
+          echo "::set-output name=dock_image::$dock_image"
+          echo "::set-output name=repo::$repo"
+
+      - uses: actions/checkout@v2
+      - uses: docker/setup-buildx-action@v1
+      - name: Cache Docker layers
+        uses: actions/cache@v2
+        with:
+          path: /tmp/.buildx-cache
+          key: ${{ runner.os }}-buildx-${{ github.sha }}
+          restore-keys: |
+            ${{ runner.os }}-buildx-
+
+      - name: Login to DockerHub
+        id: dockerhub_login
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+          
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v1 
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build and push
+        uses: docker/build-push-action@v2
+        id: docker_build
+        with:
+          context: .
+          file: ./Dockerfile
+          tags: |
+            docker.io/${{ steps.determine.outputs.dock_image }}
+            ghcr.io/${{ steps.determine.outputs.dock_image }}
+          push: true
+          cache-from: type=local,src=/tmp/.buildx-cache
+          cache-to: type=local,dest=/tmp/.buildx-cache
+
+      - name: Update DockerHub description
+        uses: peter-evans/dockerhub-description@v2
+        continue-on-error: true  # it is not crucial that this works
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+          short-description: ${{ steps.pluginmeta.outputs.title }}
+          readme-filepath: ./README.md
+          repository: ${{ steps.determine.outputs.repo }}
+
+      - name: Upload to ChRIS Store
+        if: github.event_name == 'release'
+        uses: FNNDSC/chrisstore-action@master
+        with:
+          descriptor_file: chris_plugin_info.json
+          auth: ${{ secrets.CHRIS_STORE_USER }}
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..32aa5bb
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,10 @@
+.idea/
+
+### Rust template
+# Generated by Cargo
+# will have compiled files and executables
+debug/
+target/
+
+# These are backup files generated by rustfmt
+**/*.rs.bk
diff --git a/Cargo.lock b/Cargo.lock
new file mode 100644
index 0000000..3b4a591
--- /dev/null
+++ b/Cargo.lock
@@ -0,0 +1,311 @@
+# This file is automatically @generated by Cargo.
+# It is not intended for manual editing.
+version = 3
+
+[[package]]
+name = "aho-corasick"
+version = "0.7.18"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1e37cfd5e7657ada45f742d6e99ca5788580b5c529dc78faf11ece6dc702656f"
+dependencies = [
+ "memchr",
+]
+
+[[package]]
+name = "ansi_term"
+version = "0.12.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d52a9bb7ec0cf484c551830a7ce27bd20d67eac647e1befb56b0be4ee39a55d2"
+dependencies = [
+ "winapi",
+]
+
+[[package]]
+name = "anyhow"
+version = "1.0.56"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4361135be9122e0870de935d7c439aef945b9f9ddd4199a553b5270b49c82a27"
+
+[[package]]
+name = "atty"
+version = "0.2.14"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d9b39be18770d11421cdb1b9947a45dd3f37e93092cbf377614828a319d5fee8"
+dependencies = [
+ "hermit-abi",
+ "libc",
+ "winapi",
+]
+
+[[package]]
+name = "autocfg"
+version = "1.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa"
+
+[[package]]
+name = "bitflags"
+version = "1.3.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a"
+
+[[package]]
+name = "bulkrename"
+version = "0.1.0"
+dependencies = [
+ "ansi_term",
+ "anyhow",
+ "clap",
+ "fs_extra",
+ "lazy_static",
+ "regex",
+ "walkdir",
+]
+
+[[package]]
+name = "clap"
+version = "3.1.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d8c93436c21e4698bacadf42917db28b23017027a4deccb35dbe47a7e7840123"
+dependencies = [
+ "atty",
+ "bitflags",
+ "clap_derive",
+ "indexmap",
+ "lazy_static",
+ "os_str_bytes",
+ "strsim",
+ "termcolor",
+ "textwrap",
+]
+
+[[package]]
+name = "clap_derive"
+version = "3.1.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "da95d038ede1a964ce99f49cbe27a7fb538d1da595e4b4f70b8c8f338d17bf16"
+dependencies = [
+ "heck",
+ "proc-macro-error",
+ "proc-macro2",
+ "quote",
+ "syn",
+]
+
+[[package]]
+name = "fs_extra"
+version = "1.2.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2022715d62ab30faffd124d40b76f4134a550a87792276512b18d63272333394"
+
+[[package]]
+name = "hashbrown"
+version = "0.11.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ab5ef0d4909ef3724cc8cce6ccc8572c5c817592e9285f5464f8e86f8bd3726e"
+
+[[package]]
+name = "heck"
+version = "0.4.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2540771e65fc8cb83cd6e8a237f70c319bd5c29f78ed1084ba5d50eeac86f7f9"
+
+[[package]]
+name = "hermit-abi"
+version = "0.1.19"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "62b467343b94ba476dcb2500d242dadbb39557df889310ac77c5d99100aaac33"
+dependencies = [
+ "libc",
+]
+
+[[package]]
+name = "indexmap"
+version = "1.8.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "282a6247722caba404c065016bbfa522806e51714c34f5dfc3e4a3a46fcb4223"
+dependencies = [
+ "autocfg",
+ "hashbrown",
+]
+
+[[package]]
+name = "lazy_static"
+version = "1.4.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646"
+
+[[package]]
+name = "libc"
+version = "0.2.119"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1bf2e165bb3457c8e098ea76f3e3bc9db55f87aa90d52d0e6be741470916aaa4"
+
+[[package]]
+name = "memchr"
+version = "2.4.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "308cc39be01b73d0d18f82a0e7b2a3df85245f84af96fdddc5d202d27e47b86a"
+
+[[package]]
+name = "os_str_bytes"
+version = "6.0.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8e22443d1643a904602595ba1cd8f7d896afe56d26712531c5ff73a15b2fbf64"
+dependencies = [
+ "memchr",
+]
+
+[[package]]
+name = "proc-macro-error"
+version = "1.0.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "da25490ff9892aab3fcf7c36f08cfb902dd3e71ca0f9f9517bea02a73a5ce38c"
+dependencies = [
+ "proc-macro-error-attr",
+ "proc-macro2",
+ "quote",
+ "syn",
+ "version_check",
+]
+
+[[package]]
+name = "proc-macro-error-attr"
+version = "1.0.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a1be40180e52ecc98ad80b184934baf3d0d29f979574e439af5a55274b35f869"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "version_check",
+]
+
+[[package]]
+name = "proc-macro2"
+version = "1.0.36"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c7342d5883fbccae1cc37a2353b09c87c9b0f3afd73f5fb9bba687a1f733b029"
+dependencies = [
+ "unicode-xid",
+]
+
+[[package]]
+name = "quote"
+version = "1.0.15"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "864d3e96a899863136fc6e99f3d7cae289dafe43bf2c5ac19b70df7210c0a145"
+dependencies = [
+ "proc-macro2",
+]
+
+[[package]]
+name = "regex"
+version = "1.5.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1a11647b6b25ff05a515cb92c365cec08801e83423a235b51e231e1808747286"
+dependencies = [
+ "aho-corasick",
+ "memchr",
+ "regex-syntax",
+]
+
+[[package]]
+name = "regex-syntax"
+version = "0.6.25"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f497285884f3fcff424ffc933e56d7cbca511def0c9831a7f9b5f6153e3cc89b"
+
+[[package]]
+name = "same-file"
+version = "1.0.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "93fc1dc3aaa9bfed95e02e6eadabb4baf7e3078b0bd1b4d7b6b0b68378900502"
+dependencies = [
+ "winapi-util",
+]
+
+[[package]]
+name = "strsim"
+version = "0.10.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "73473c0e59e6d5812c5dfe2a064a6444949f089e20eec9a2e5506596494e4623"
+
+[[package]]
+name = "syn"
+version = "1.0.86"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8a65b3f4ffa0092e9887669db0eae07941f023991ab58ea44da8fe8e2d511c6b"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "unicode-xid",
+]
+
+[[package]]
+name = "termcolor"
+version = "1.1.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "bab24d30b911b2376f3a13cc2cd443142f0c81dda04c118693e35b3835757755"
+dependencies = [
+ "winapi-util",
+]
+
+[[package]]
+name = "textwrap"
+version = "0.15.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b1141d4d61095b28419e22cb0bbf02755f5e54e0526f97f1e3d1d160e60885fb"
+
+[[package]]
+name = "unicode-xid"
+version = "0.2.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8ccb82d61f80a663efe1f787a51b16b5a51e3314d6ac365b08639f52387b33f3"
+
+[[package]]
+name = "version_check"
+version = "0.9.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f"
+
+[[package]]
+name = "walkdir"
+version = "2.3.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "808cf2735cd4b6866113f648b791c6adc5714537bc222d9347bb203386ffda56"
+dependencies = [
+ "same-file",
+ "winapi",
+ "winapi-util",
+]
+
+[[package]]
+name = "winapi"
+version = "0.3.9"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419"
+dependencies = [
+ "winapi-i686-pc-windows-gnu",
+ "winapi-x86_64-pc-windows-gnu",
+]
+
+[[package]]
+name = "winapi-i686-pc-windows-gnu"
+version = "0.4.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6"
+
+[[package]]
+name = "winapi-util"
+version = "0.1.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "70ec6ce85bb158151cae5e5c87f95a8e97d2c0c4b001223f33a334e3ce5de178"
+dependencies = [
+ "winapi",
+]
+
+[[package]]
+name = "winapi-x86_64-pc-windows-gnu"
+version = "0.4.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f"
diff --git a/Cargo.toml b/Cargo.toml
new file mode 100644
index 0000000..f63420d
--- /dev/null
+++ b/Cargo.toml
@@ -0,0 +1,21 @@
+[package]
+name = "bulkrename"
+version = "0.1.0"
+edition = "2021"
+
+readme = "README.md"
+description = "Bulk rename ChRIS ds plugin"
+repository = "https://github.com/FNNDSC/pl-bulk-rename"
+license = "MIT"
+categories = ["command-line-utilities"]
+
+# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
+
+[dependencies]
+clap = { version = "3.1.6", features = ["derive"] }
+fs_extra = "1.2.0"
+regex = "1.5.5"
+ansi_term = "0.12"
+walkdir = "2.3.2"
+anyhow = "1.0.56"
+lazy_static = "1.4.0"
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..efa8eeb
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,11 @@
+FROM rust:1.59-slim-bullseye as builder
+WORKDIR /usr/local/src/bulkrename
+COPY . .
+RUN cargo build --release
+RUN strip target/release/bulkrename
+
+FROM debian:bullseye-slim
+COPY --from=builder /usr/local/src/bulkrename/target/release/bulkrename /usr/local/bin/bulkrename
+COPY /docker-entrypoint.sh /docker-entrypoint.sh
+COPY chris_plugin_info.json /chris_plugin_info.json
+CMD ["bulkrename"]
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..4278d89
--- /dev/null
+++ b/README.md
@@ -0,0 +1,69 @@
+# Bulk Rename
+
+[![Version](https://img.shields.io/docker/v/fnndsc/pl-bulk-rename?sort=semver)](https://hub.docker.com/r/fnndsc/pl-bulk-rename)
+[![MIT License](https://img.shields.io/github/license/fnndsc/pl-bulk-rename)](https://github.com/FNNDSC/pl-bulk-rename/blob/main/LICENSE)
+[![ci](https://github.com/FNNDSC/pl-bulk-rename/actions/workflows/ci.yml/badge.svg)](https://github.com/FNNDSC/pl-bulk-rename/actions/workflows/ci.yml)
+
+`pl-bulk-rename` is a [_ChRIS_](https://chrisproject.org/)
+_ds_ plugin which copies files from an input directory to an
+output directory under different names using regular expressions.
+
+## Installation
+
+`pl-bulk-rename` is a _[ChRIS](https://chrisproject.org/) plugin_, meaning it can
+run from either within _ChRIS_ or the command-line.
+
+[![Get it from chrisstore.co](https://ipfs.babymri.org/ipfs/QmaQM9dUAYFjLVn3PpNTrpbKVavvSTxNLE5BocRCW1UoXG/light.png)](https://chrisstore.co/plugin/pl-bulk-rename)
+
+## Usage
+
+Regular expression syntax is based on the [regex](https://crates.io/crates/regex) crate.
+See https://docs.rs/regex/1.5.5/regex/#grouping-and-flags
+
+### Local Usage
+
+To get started with local command-line usage, use [Apptainer](https://apptainer.org/)
+(a.k.a. Singularity) to run `pl-bulk-rename` as a container.
+
+To print its available options, run:
+
+```shell
+singularity exec docker://fnndsc/pl-bulk-rename bulkrename --help
+```
+
+## Examples
+
+`bulkrename` copies data from an input directory to an output directory.
+
+Consider the data in [`examples/input`](examples/input):
+
+```
+examples/input
+├── a
+│   ├── food.txt
+│   └── log
+├── b
+│   ├── food.txt
+│   └── log
+└── c
+    ├── food.txt
+    └── log
+```
+
+To rename every `.txt` file to have the name of their parent directory:
+
+```shell
+bulkrename --filter '.*\.txt' \
+           --expression '^(.*?)/(.*?)\.txt$' \
+           --replace '$1.txt' \
+           examples/input examples/filewise
+```
+
+To rename the subdirectories `a`, `b`, `c`, of the input directory to have a prefix `pear_`:
+
+```shell
+bulkrename --filter '^[abc]$' \
+           --expression '([abc])' \
+           --replace 'pear_$1' \
+           examples/input examples/dirwise
+```
diff --git a/chris_plugin_info.json b/chris_plugin_info.json
new file mode 100644
index 0000000..01f53c5
--- /dev/null
+++ b/chris_plugin_info.json
@@ -0,0 +1,57 @@
+{
+  "type": "ds",
+  "parameters": [
+    {
+      "name": "filter",
+      "type": "str",
+      "optional": true,
+      "flag": "--filter",
+      "short_flag": "-f",
+      "action": "store",
+      "help": "Input path filter. Paths which do not match this regex are excluded.",
+      "default": ".*",
+      "ui_exposed": true
+    },
+    {
+      "name": "expression",
+      "type": "str",
+      "optional": true,
+      "flag": "--expression",
+      "short_flag": "-e",
+      "action": "store",
+      "help": "Regular expression to match paths. See https://docs.rs/regex/1.5.5/regex/#syntax",
+      "default": "(.*)",
+      "ui_exposed": true
+    },
+    {
+      "name": "replacement",
+      "type": "str",
+      "optional": true,
+      "flag": "--replace",
+      "short_flag": "-r",
+      "action": "store",
+      "help": "Replacement string with capture groups. See https://docs.rs/regex/1.5.5/regex/#grouping-and-flags",
+      "default": "\\1",
+      "ui_exposed": true
+    }
+  ],
+  "icon": "",
+  "authors": "FNNDSC <dev@babyMRI.org>",
+  "title": "Bulk Rename",
+  "category": "Utility",
+  "description": "A ChRIS plugin to rename paths using regex",
+  "documentation": "https://github.com/FNNDSC/pl-bulk-rename",
+  "license": "MIT",
+  "version": "0.1.0",
+  "selfpath": "/usr/local/bin",
+  "selfexec": "bulkrename",
+  "execshell": "/docker-entrypoint.sh",
+  "min_number_of_workers": 1,
+  "max_number_of_workers": 1,
+  "min_memory_limit": "",
+  "max_memory_limit": "",
+  "min_cpu_limit": "",
+  "max_cpu_limit": "",
+  "min_gpu_limit": 0,
+  "max_gpu_limit": 0
+}
diff --git a/docker-entrypoint.sh b/docker-entrypoint.sh
new file mode 100755
index 0000000..d0747ea
--- /dev/null
+++ b/docker-entrypoint.sh
@@ -0,0 +1,7 @@
+#!/bin/sh
+# CUBE **requires** all of selfpath, selfexec, and execshell to be defined,
+# which doesn't make sense for binary applications like this one.
+# `docker-entrypoint.sh` is a script which transparently executes its
+# arguments as a command.
+
+exec "$@"
diff --git a/examples/dirwise/pear_a/food.txt b/examples/dirwise/pear_a/food.txt
new file mode 100644
index 0000000..4c479de
--- /dev/null
+++ b/examples/dirwise/pear_a/food.txt
@@ -0,0 +1 @@
+apple
diff --git a/examples/dirwise/pear_a/log b/examples/dirwise/pear_a/log
new file mode 100644
index 0000000..eb7de92
--- /dev/null
+++ b/examples/dirwise/pear_a/log
@@ -0,0 +1 @@
+the food is "apple"
diff --git a/examples/dirwise/pear_b/food.txt b/examples/dirwise/pear_b/food.txt
new file mode 100644
index 0000000..0ebdb91
--- /dev/null
+++ b/examples/dirwise/pear_b/food.txt
@@ -0,0 +1 @@
+bread
diff --git a/examples/dirwise/pear_b/log b/examples/dirwise/pear_b/log
new file mode 100644
index 0000000..2311e62
--- /dev/null
+++ b/examples/dirwise/pear_b/log
@@ -0,0 +1 @@
+the food is "bread"
diff --git a/examples/dirwise/pear_c/food.txt b/examples/dirwise/pear_c/food.txt
new file mode 100644
index 0000000..871bb87
--- /dev/null
+++ b/examples/dirwise/pear_c/food.txt
@@ -0,0 +1 @@
+cookie
diff --git a/examples/dirwise/pear_c/log b/examples/dirwise/pear_c/log
new file mode 100644
index 0000000..89a352a
--- /dev/null
+++ b/examples/dirwise/pear_c/log
@@ -0,0 +1 @@
+the food is "cookie"
diff --git a/examples/filewise/a.txt b/examples/filewise/a.txt
new file mode 100644
index 0000000..4c479de
--- /dev/null
+++ b/examples/filewise/a.txt
@@ -0,0 +1 @@
+apple
diff --git a/examples/filewise/b.txt b/examples/filewise/b.txt
new file mode 100644
index 0000000..0ebdb91
--- /dev/null
+++ b/examples/filewise/b.txt
@@ -0,0 +1 @@
+bread
diff --git a/examples/filewise/c.txt b/examples/filewise/c.txt
new file mode 100644
index 0000000..871bb87
--- /dev/null
+++ b/examples/filewise/c.txt
@@ -0,0 +1 @@
+cookie
diff --git a/examples/input/a/food.txt b/examples/input/a/food.txt
new file mode 100644
index 0000000..4c479de
--- /dev/null
+++ b/examples/input/a/food.txt
@@ -0,0 +1 @@
+apple
diff --git a/examples/input/a/log b/examples/input/a/log
new file mode 100644
index 0000000..eb7de92
--- /dev/null
+++ b/examples/input/a/log
@@ -0,0 +1 @@
+the food is "apple"
diff --git a/examples/input/b/food.txt b/examples/input/b/food.txt
new file mode 100644
index 0000000..0ebdb91
--- /dev/null
+++ b/examples/input/b/food.txt
@@ -0,0 +1 @@
+bread
diff --git a/examples/input/b/log b/examples/input/b/log
new file mode 100644
index 0000000..2311e62
--- /dev/null
+++ b/examples/input/b/log
@@ -0,0 +1 @@
+the food is "bread"
diff --git a/examples/input/c/food.txt b/examples/input/c/food.txt
new file mode 100644
index 0000000..871bb87
--- /dev/null
+++ b/examples/input/c/food.txt
@@ -0,0 +1 @@
+cookie
diff --git a/examples/input/c/log b/examples/input/c/log
new file mode 100644
index 0000000..89a352a
--- /dev/null
+++ b/examples/input/c/log
@@ -0,0 +1 @@
+the food is "cookie"
diff --git a/src/main.rs b/src/main.rs
new file mode 100644
index 0000000..44b7af7
--- /dev/null
+++ b/src/main.rs
@@ -0,0 +1,152 @@
+use std::path::{PathBuf};
+use clap::{Parser};
+use regex::{Regex};
+use walkdir::{WalkDir};
+use anyhow::{Context, Result, Ok, bail};
+use ansi_term::{ANSIString};
+use ansi_term::Style;
+use ansi_term::Colour::{Cyan, Green};
+use std::fs::create_dir_all;
+use fs_extra;
+use lazy_static::lazy_static;
+
+#[derive(Parser)]
+#[clap(author, version,
+about = "Bulk rename using regular expressions",
+long_about = "A fast and simple tool for copying data from an input directory to an output directory under different paths based on regular expressions.\nThe syntax is based on the \"regex\" crate: see https://docs.rs/regex/1.5.5/regex/#grouping-and-flags",
+propagate_version = true,
+disable_help_subcommand = true
+)]
+struct Cli {
+    /// Input path filter. Paths which do not match this regex are excluded.
+    #[clap(short, long, default_value = ".*")]
+    filter: String,
+
+    /// Regular expression to match paths
+    #[clap(short, long, default_value = "(.*)")]
+    expression: String,
+
+    /// Replacement string with capture groups
+    #[clap(short, long, default_value = "$0")]
+    replace: String,
+
+    /// Silence output
+    #[clap(short, long)]
+    quiet: bool,
+
+    /// deprecated ChRIS flag. Does nothing.
+    #[clap(long)]
+    saveinputmeta: bool,
+
+    /// deprecated ChRIS flag. Does nothing.
+    #[clap(long)]
+    saveoutputmeta: bool,
+
+    /// input directory
+    #[clap()]
+    input_dir: PathBuf,
+
+    /// output directory
+    #[clap()]
+    output_dir: PathBuf,
+}
+
+
+fn main() -> Result<()> {
+    let args: Cli = Cli::parse();
+
+    if !args.input_dir.is_dir() {
+        bail!("not a directory: {:?}", args.input_dir);
+    }
+    if !args.output_dir.is_dir() {
+        bail!("not a directory: {:?}", args.output_dir);
+    }
+    if !args.output_dir.read_dir()?.next().is_none() {
+        bail!("not empty: {:?}", args.output_dir);
+    }
+
+    let filter = Regex::new(&args.filter)
+        .with_context(|| format!("Invalid option --filter={}", &args.filter))?;
+    let expression = Regex::new(&args.expression)
+        .with_context(|| format!("Invalid option --expression={}", &args.expression))?;
+
+    let input_pre = args.input_dir.to_str().unwrap();
+    let output_pre = args.output_dir.to_str().unwrap();
+
+    let mut did_nothing = true;
+
+    for (rel, input_path) in filter_input_dir(&args.input_dir, &filter) {
+        let renamed = expression.replace(rel.to_str().unwrap(), &args.replace).to_string();
+        let output_path = args.output_dir.join(&renamed);
+
+        if output_path.exists() {
+            bail!(
+                "{:?} already exists. Hint: to operate on subdirectories, try --filter='^{}$'",
+                &output_path,
+                args.filter
+            );
+        }
+
+        cpr(&input_path, &output_path)?;
+        pretty_print(input_pre, output_pre, &rel, &renamed);
+        did_nothing = false;
+    }
+
+    if did_nothing {
+        bail!("No paths under {:?} matched by --filter={}", &args.input_dir, &args.filter)
+    }
+    Ok(())
+}
+
+/// Pretty much `cp -r $1 $2`
+fn cpr(src: &PathBuf, dst: &PathBuf) -> Result<()> {
+    let parent_dir = dst.parent().unwrap();
+    create_dir_all(parent_dir)
+        .with_context(|| format!("Could not create parent directory {:?}", parent_dir))?;
+    if src.is_file() {
+        fs_extra::file::copy(src, dst, &*FILE_COPY_OPTIONS)?;
+    }
+    else if src.is_dir() {
+        fs_extra::dir::copy(src, dst, &*DIR_COPY_OPTIONS)?;
+    }
+    else {
+        bail!("{:?} is not a file nor directory", src);
+    }
+    Ok(())
+}
+
+
+/// produce relative subpaths under a directory which match a regex
+fn filter_input_dir<'a>(
+    input_dir: &'a PathBuf, filter: &'a Regex
+) -> impl Iterator<Item = (PathBuf, PathBuf)> +'a {
+    WalkDir::new(input_dir).into_iter()
+        .map(|e| e.unwrap().into_path())
+        .map(move |p| ((p.strip_prefix(input_dir).unwrap()).to_owned(), p))
+        .filter(|e| filter.is_match(e.0.to_string_lossy().as_ref()))
+}
+
+fn pretty_print(input_pre: &str, output_pre: &str, src: &PathBuf, dst: &str) {
+    println!(
+        "{}/{} {} {}/{}",
+        input_pre,
+        Cyan.paint(src.to_str().unwrap()),
+        *DIM_ARROW,
+        output_pre,
+        Green.paint(dst)
+    )
+}
+
+lazy_static! {
+    static ref DIM_ARROW: ANSIString<'static> = Style::new().dimmed().paint("->");
+    static ref FILE_COPY_OPTIONS: fs_extra::file::CopyOptions = fs_extra::file::CopyOptions::new();
+    // static ref DIR_COPY_OPTIONS: fs_extra::dir::CopyOptions = fs_extra::dir::CopyOptions::new();
+    static ref DIR_COPY_OPTIONS: fs_extra::dir::CopyOptions = fs_extra::dir::CopyOptions{
+        overwrite: false,
+        skip_exist: false,
+        buffer_size: 64000,
+        copy_inside: true,
+        content_only: true,
+        depth: 0
+    };
+}