diff --git a/environment.yaml b/environment.yaml
new file mode 100644
index 0000000..82318a6
--- /dev/null
+++ b/environment.yaml
@@ -0,0 +1,11 @@
+# only put tools that are needed for tests (e.g., `bowtie-build` is needed to make sure
+# that bowtie-index worked), not for the wrappers themselves, which should have
+# their own environment.yml files.
+dependencies:
+  - bioconda::bowtie2 ==2.3.0
+  - bioconda::gffutils ==0.8.7.1
+  - bioconda::hisat2 ==2.0.5
+  - bioconda::pytest ==3.0.5
+  - bioconda::snakemake ==3.11.2
+  - bioconda::samtools ==1.4
+  - lcdb::lcdblib ==0.1
diff --git a/pip-requirements.txt b/pip-requirements.txt
deleted file mode 100644
index e69de29..0000000
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index 27ab3d0..0000000
--- a/requirements.txt
+++ /dev/null
@@ -1,11 +0,0 @@
-# only put tools that are needed for tests (e.g., `bowtie-build` is needed to make sure
-# that bowtie-index worked), not for the wrappers themselves, which should have
-# their own environment.yml files.
-bowtie2 ==2.3.0
-gffutils ==0.8.7.1
-hisat2 ==2.0.5
-lcdblib ==0.1
-pysam ==0.9.1.4
-pytest ==3.0.5
-samtools ==1.3.1
-snakemake ==3.10.1
diff --git a/test/test_bowtie2.py b/test/test_bowtie2.py
index bdbcb7b..03564f3 100644
--- a/test/test_bowtie2.py
+++ b/test/test_bowtie2.py
@@ -1,5 +1,4 @@
 import pytest
-import pysam
 from snakemake.shell import shell
 from lcdblib.snakemake import aligners
 from utils import run, dpath, rm, symlink_in_tempdir
diff --git a/test/test_hisat2.py b/test/test_hisat2.py
index 38cdd76..cd076f3 100644
--- a/test/test_hisat2.py
+++ b/test/test_hisat2.py
@@ -1,5 +1,4 @@
 import pytest
-import pysam
 from snakemake.shell import shell
 from lcdblib.snakemake import aligners
 from utils import run, dpath, rm, symlink_in_tempdir
diff --git a/test/test_kallisto.py b/test/test_kallisto.py
index 0075b16..d3960d2 100644
--- a/test/test_kallisto.py
+++ b/test/test_kallisto.py
@@ -1,6 +1,5 @@
 import pytest
 import json
-import pysam
 from snakemake.shell import shell
 from lcdblib.snakemake import aligners
 from utils import run, dpath, rm, symlink_in_tempdir
diff --git a/travis-setup.sh b/travis-setup.sh
index da31fbe..8deb7ca 100755
--- a/travis-setup.sh
+++ b/travis-setup.sh
@@ -15,5 +15,4 @@ conda config --add channels bioconda
 conda config --add channels lcdb
 
 conda install -y python=3.5
-conda install -y --file requirements.txt
-pip install -r pip-requirements.txt
+conda env update -n root --file environment.yaml
diff --git a/wrappers/bowtie2/align/environment.yaml b/wrappers/bowtie2/align/environment.yaml
index e1502f8..efc1dca 100644
--- a/wrappers/bowtie2/align/environment.yaml
+++ b/wrappers/bowtie2/align/environment.yaml
@@ -3,5 +3,5 @@ channels:
   - lcdb
 dependencies:
   - bowtie2 ==2.3.0
-  - samtools ==1.3.1
+  - samtools ==1.4
   - lcdblib ==0.1
diff --git a/wrappers/hisat2/align/environment.yaml b/wrappers/hisat2/align/environment.yaml
index 1672920..f5da994 100644
--- a/wrappers/hisat2/align/environment.yaml
+++ b/wrappers/hisat2/align/environment.yaml
@@ -3,5 +3,5 @@ channels:
   - lcdb
 dependencies:
   - hisat2 ==2.0.5
-  - samtools ==1.3.1
+  - samtools ==1.4
   - lcdblib ==0.1
diff --git a/wrappers/rseqc/bam_stat/environment.yaml b/wrappers/rseqc/bam_stat/environment.yaml
index 89166f4..ac0578f 100644
--- a/wrappers/rseqc/bam_stat/environment.yaml
+++ b/wrappers/rseqc/bam_stat/environment.yaml
@@ -3,3 +3,4 @@ channels:
   - r
 dependencies:
   - rseqc ==2.6.4
+  - pysam ==0.10.0
diff --git a/wrappers/rseqc/geneBody_coverage/environment.yaml b/wrappers/rseqc/geneBody_coverage/environment.yaml
index e6a2e7f..7ddc0c9 100644
--- a/wrappers/rseqc/geneBody_coverage/environment.yaml
+++ b/wrappers/rseqc/geneBody_coverage/environment.yaml
@@ -5,4 +5,5 @@ channels:
   - conda-forge
 dependencies:
   - rseqc ==2.6.4
+  - pysam ==0.10.0
   - r-essentials ==1.5.1
diff --git a/wrappers/rseqc/infer_experiment/environment.yaml b/wrappers/rseqc/infer_experiment/environment.yaml
index 89166f4..ac0578f 100644
--- a/wrappers/rseqc/infer_experiment/environment.yaml
+++ b/wrappers/rseqc/infer_experiment/environment.yaml
@@ -3,3 +3,4 @@ channels:
   - r
 dependencies:
   - rseqc ==2.6.4
+  - pysam ==0.10.0
diff --git a/wrappers/rseqc/tin/environment.yaml b/wrappers/rseqc/tin/environment.yaml
index 89166f4..ac0578f 100644
--- a/wrappers/rseqc/tin/environment.yaml
+++ b/wrappers/rseqc/tin/environment.yaml
@@ -3,3 +3,4 @@ channels:
   - r
 dependencies:
   - rseqc ==2.6.4
+  - pysam ==0.10.0
diff --git a/wrappers/samtools/index/environment.yaml b/wrappers/samtools/index/environment.yaml
index 69c397b..4956f4d 100644
--- a/wrappers/samtools/index/environment.yaml
+++ b/wrappers/samtools/index/environment.yaml
@@ -1,4 +1,4 @@
 channels:
   - bioconda
 dependencies:
-  - samtools ==1.3.1
+  - samtools ==1.4
diff --git a/wrappers/samtools/sort/environment.yaml b/wrappers/samtools/sort/environment.yaml
index 69c397b..4956f4d 100644
--- a/wrappers/samtools/sort/environment.yaml
+++ b/wrappers/samtools/sort/environment.yaml
@@ -1,4 +1,4 @@
 channels:
   - bioconda
 dependencies:
-  - samtools ==1.3.1
+  - samtools ==1.4