diff --git a/recipes/phantompeakqualtools/build.sh b/recipes/phantompeakqualtools/build.sh
new file mode 100644
index 0000000000000..70513538e3d1a
--- /dev/null
+++ b/recipes/phantompeakqualtools/build.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+
+#add shebang to make directly executable
+cat <(
+      echo '#!/usr/bin/env Rscript'
+    ) run_spp.R \
+> $PREFIX/bin/run_spp.R
+
+chmod +x $PREFIX/bin/run_spp.R
+
diff --git a/recipes/phantompeakqualtools/meta.yaml b/recipes/phantompeakqualtools/meta.yaml
new file mode 100644
index 0000000000000..6da9cbd939c8a
--- /dev/null
+++ b/recipes/phantompeakqualtools/meta.yaml
@@ -0,0 +1,39 @@
+{% set version = "1.2" %}
+{% set sha256 = "86cbcca80b65f150b1cdbea673d8a47caba88c2db6b3b567a80f2c797c9a1668" %}
+
+package:
+  name: phantompeakqualtools
+  version: {{ version }}
+
+source:
+  url: https://github.com/kundajelab/phantompeakqualtools/archive/{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+
+build:
+  number: 0
+
+requirements:
+  run:
+    - r-base >=3.1
+    - r-catools
+    - r-snow
+    - r-snowfall
+    - r-bitops
+    - r-spp >=1.13
+    - bioconductor-rsamtools
+    - boost
+    - samtools
+
+test:
+  commands:
+    - run_spp.R 2>&1 | grep MANDATORY
+
+about:
+  home: https://github.com/kundajelab/phantompeakqualtools
+  license: BSD-3-Clause
+  summary:  This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays. 
+
+extra:
+  identifiers:
+    - doi:10.1101/gr.136184.111
+    - doi:10.1038/nbt.1508