diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 2cb2d24a3..270fd53df 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -44,6 +44,10 @@ jobs:
     - run: conda list
     - run: pytest -c pytest.python3.ini --cov=augur
     - run: cram --shell=/bin/bash tests/functional/*.t tests/builds/*.t
+      env:
+        AUGUR: coverage run -a ${{ github.workspace }}/bin/augur
+        COVERAGE_FILE: ${{ github.workspace }}/.coverage
+        COVERAGE_RCFILE: ${{ github.workspace }}/.coveragerc
     - run: coverage xml
     - run: bash tests/builds/runner.sh
     - if: github.repository == 'nextstrain/augur' && matrix.python-version == '3.10' && matrix.biopython-version == ''
diff --git a/tests/builds/zika.t b/tests/builds/zika.t
index 70aa9bb0d..55f8b2c93 100644
--- a/tests/builds/zika.t
+++ b/tests/builds/zika.t
@@ -7,8 +7,7 @@ Running from the test data directory allows us to use relative paths that won't
   $ TEST_DATA_DIR="$TESTDIR/zika"
   $ mkdir -p "$TMP/out"
   $ pushd "$TEST_DATA_DIR" > /dev/null
-  $ export COVERAGE_FILE="$TESTDIR/../../.coverage"
-  $ export AUGUR="coverage run -a --rcfile=$TESTDIR/../../.coveragerc ../../../bin/augur"
+  $ export AUGUR="${AUGUR:-../../../bin/augur}"
 
 Parse a FASTA whose defline contains metadata into separate sequence and metadata files.
 
diff --git a/tests/builds/zika_compressed.t b/tests/builds/zika_compressed.t
index 8b0fba7dc..be39ce704 100644
--- a/tests/builds/zika_compressed.t
+++ b/tests/builds/zika_compressed.t
@@ -7,8 +7,7 @@ Running from the test data directory allows us to use relative paths that won't
   $ TEST_DATA_DIR="$TESTDIR/zika"
   $ mkdir -p "$TMP/out"
   $ pushd "$TEST_DATA_DIR" > /dev/null
-  $ export COVERAGE_FILE="$TESTDIR/../../.coverage"
-  $ export AUGUR="coverage run -a --rcfile=$TESTDIR/../../.coveragerc ../../../bin/augur"
+  $ export AUGUR="${AUGUR:-../../../bin/augur}"
 
 Parse a FASTA whose defline contains metadata into separate sequence and metadata files.
 
diff --git a/tests/functional/ancestral.t b/tests/functional/ancestral.t
index f51d2e6ca..649029879 100644
--- a/tests/functional/ancestral.t
+++ b/tests/functional/ancestral.t
@@ -1,8 +1,7 @@
 Integration tests for augur ancestral.
 
   $ pushd "$TESTDIR" > /dev/null
-  $ export COVERAGE_FILE="$TESTDIR/../../.coverage"
-  $ export AUGUR="coverage run -a --rcfile=$TESTDIR/../../.coveragerc ../../bin/augur"
+  $ export AUGUR="${AUGUR:-../../bin/augur}"
 
 Infer ancestral sequences for the given tree and alignment.
 The default is to infer ambiguous bases, so there should not be N bases in the inferred output sequences.
diff --git a/tests/functional/clades.t b/tests/functional/clades.t
index 24e3e1d38..619c35d56 100644
--- a/tests/functional/clades.t
+++ b/tests/functional/clades.t
@@ -1,8 +1,7 @@
 Integration tests for augur clades.
 
   $ pushd "$TESTDIR" > /dev/null
-  $ export COVERAGE_FILE="$TESTDIR/../../.coverage"
-  $ export AUGUR="coverage run -a --rcfile=$TESTDIR/../../.coveragerc ../../bin/augur"
+  $ export AUGUR="${AUGUR:-../../bin/augur}"
 
 Test augur clades with simple Zika input files and hierarchical clades.
 
@@ -14,4 +13,4 @@ Test augur clades with simple Zika input files and hierarchical clades.
 
   $ python3 "$TESTDIR/../../scripts/diff_jsons.py"  clades/clades.json "$TMP/clades.json" \
   >   --exclude-paths "root['generated_by']"
-  {}
+  {}
\ No newline at end of file
diff --git a/tests/functional/export_v2.t b/tests/functional/export_v2.t
index ea4c517c0..39cf13101 100644
--- a/tests/functional/export_v2.t
+++ b/tests/functional/export_v2.t
@@ -1,8 +1,7 @@
 Integration tests for augur export v2.
 
   $ pushd "$TESTDIR" > /dev/null
-  $ export COVERAGE_FILE="$TESTDIR/../../.coverage"
-  $ export AUGUR="coverage run -a --rcfile=$TESTDIR/../../.coveragerc ../../bin/augur"
+  $ export AUGUR="${AUGUR:-../../bin/augur}"
 
 Minimal export
 
diff --git a/tests/functional/filter.t b/tests/functional/filter.t
index ff25defb7..120e57a93 100644
--- a/tests/functional/filter.t
+++ b/tests/functional/filter.t
@@ -1,8 +1,7 @@
 Integration tests for augur filter.
 
   $ pushd "$TESTDIR" > /dev/null
-  $ export COVERAGE_FILE="$TESTDIR/../../.coverage"
-  $ export AUGUR="coverage run -a --rcfile=$TESTDIR/../../.coveragerc ../../bin/augur"
+  $ export AUGUR="${AUGUR:-../../bin/augur}"
 
 Filter with exclude query for two regions that comprise all but one strain.
 This filter should leave a single record from Oceania.
diff --git a/tests/functional/frequencies.t b/tests/functional/frequencies.t
index 196c09fe3..937e240d2 100644
--- a/tests/functional/frequencies.t
+++ b/tests/functional/frequencies.t
@@ -1,8 +1,7 @@
 Integration tests for augur frequencies.
 
   $ pushd "$TESTDIR" > /dev/null
-  $ export COVERAGE_FILE="$TESTDIR/../../.coverage"
-  $ export AUGUR="coverage run -a --rcfile=$TESTDIR/../../.coveragerc ../../bin/augur"
+  $ export AUGUR="${AUGUR:-../../bin/augur}"
 
 Calculate KDE-based tip frequencies from a refined tree.
 Timepoints used to estimate frequencies (i.e., "pivots") get calculated from the range of dates in the given metadata.
diff --git a/tests/functional/mask.t b/tests/functional/mask.t
index f99bd3e89..905f2a78b 100644
--- a/tests/functional/mask.t
+++ b/tests/functional/mask.t
@@ -1,8 +1,7 @@
 Integration tests for augur mask.
 
   $ pushd "$TESTDIR" > /dev/null
-  $ export COVERAGE_FILE="$TESTDIR/../../.coverage"
-  $ export AUGUR="coverage run -a --rcfile=$TESTDIR/../../.coveragerc ../../bin/augur"
+  $ export AUGUR="${AUGUR:-../../bin/augur}"
 
 Try masking a VCF without any specified mask.
 
diff --git a/tests/functional/parse.t b/tests/functional/parse.t
index 924be9caf..796adc5af 100644
--- a/tests/functional/parse.t
+++ b/tests/functional/parse.t
@@ -1,8 +1,7 @@
 Integration tests for augur parse.
 
   $ pushd "$TESTDIR" > /dev/null
-  $ export COVERAGE_FILE="$TESTDIR/../../.coverage"
-  $ export AUGUR="coverage run -a --rcfile=$TESTDIR/../../.coveragerc ../../bin/augur"
+  $ export AUGUR="${AUGUR:-../../bin/augur}"
 
 Parse Zika sequences into sequences and metadata.
 
diff --git a/tests/functional/refine.t b/tests/functional/refine.t
index fa15e6707..7ceeb3614 100644
--- a/tests/functional/refine.t
+++ b/tests/functional/refine.t
@@ -1,8 +1,7 @@
 Integration tests for augur refine.
 
   $ pushd "$TESTDIR" > /dev/null
-  $ export COVERAGE_FILE="$TESTDIR/../../.coverage"
-  $ export AUGUR="coverage run -a --rcfile=$TESTDIR/../../.coveragerc ../../bin/augur"
+  $ export AUGUR="${AUGUR:-../../bin/augur}"
 
 Try building a time tree.
 
diff --git a/tests/functional/traits.t b/tests/functional/traits.t
index 43fbbf9ad..5e2089c10 100644
--- a/tests/functional/traits.t
+++ b/tests/functional/traits.t
@@ -1,8 +1,7 @@
 Integration tests for augur traits.
 
   $ pushd "$TESTDIR" > /dev/null
-  $ export COVERAGE_FILE="$TESTDIR/../../.coverage"
-  $ export AUGUR="coverage run -a --rcfile=$TESTDIR/../../.coveragerc ../../bin/augur"
+  $ export AUGUR="${AUGUR:-../../bin/augur}"
 
 Infer the ancestral region for a given tree and metadata.
 
diff --git a/tests/functional/tree.t b/tests/functional/tree.t
index f7829ce47..407ed4082 100644
--- a/tests/functional/tree.t
+++ b/tests/functional/tree.t
@@ -1,8 +1,7 @@
 Integration tests for augur tree.
 
   $ pushd "$TESTDIR" > /dev/null
-  $ export COVERAGE_FILE="$TESTDIR/../../.coverage"
-  $ export AUGUR="coverage run -a --rcfile=$TESTDIR/../../.coveragerc ../../bin/augur"
+  $ export AUGUR="${AUGUR:-../../bin/augur}"
 
 Try building a tree with IQ-TREE.