diff --git a/environment.yml b/environment.yml
index cbff633c7d620574ae8241266f85a828e8a04911..6b19c0f00c5df0e7bc561f356f0beb91432d70d7 100644
--- a/environment.yml
+++ b/environment.yml
@@ -5,10 +5,10 @@ channels:
   - defaults
 dependencies:
   - python=2.7.11
-  - conda-forge::scipy=0.18.1
-  - conda-forge::numpy=1.12.1
+  - conda-forge::scipy=1.0.1
+  - conda-forge::numpy=1.14.2
   - bcbio::bx-python=0.7.3
-  - bioconda::pysam=0.8.3
+  - bioconda::pysam=0.14.1
   - cooler=0.8.3
   - bowtie2=2.3.5
   - samtools=1.9