diff --git a/pkgs/development/python-modules/pysam/default.nix b/pkgs/development/python-modules/pysam/default.nix
index 86a81d14d74..108e2dab912 100644
--- a/pkgs/development/python-modules/pysam/default.nix
+++ b/pkgs/development/python-modules/pysam/default.nix
@@ -8,14 +8,14 @@
 , htslib
 , libdeflate
 , xz
-, pytest
+, pytestCheckHook
 , samtools
 , zlib
 }:
 
 buildPythonPackage rec {
   pname   = "pysam";
-  version = "0.20.0";
+  version = "0.21.0";
 
   # Fetching from GitHub instead of PyPi cause the 0.13 src release on PyPi is
   # missing some files which cause test failures.
@@ -24,19 +24,21 @@ buildPythonPackage rec {
     owner = "pysam-developers";
     repo = "pysam";
     rev = "refs/tags/v${version}";
-    hash = "sha256-7yEZJ+iIw4qOxsanlKQlqt1bfi8MvyYjGJWiVDmXBrc=";
+    hash = "sha256-C4/AJwcUyLoUEUEnsATLHJb5F8mltP8X2XfktYu0OTo=";
   };
 
   nativeBuildInputs = [ samtools ];
+
   buildInputs = [
     bzip2
     curl
-    cython
     libdeflate
     xz
     zlib
   ];
 
+  propagatedBuildInputs = [ cython ];
+
   # Use nixpkgs' htslib instead of the bundled one
   # See https://pysam.readthedocs.io/en/latest/installation.html#external
   # NOTE that htslib should be version compatible with pysam
@@ -47,53 +49,17 @@ buildPythonPackage rec {
   '';
 
   nativeCheckInputs = [
-    pytest
+    pytestCheckHook
     bcftools
     htslib
   ];
 
-  # See https://github.com/NixOS/nixpkgs/pull/100823 for why we aren't using
-  # disabledTests and pytestFlagsArray through pytestCheckHook
-  checkPhase = ''
-    # Needed to avoid /homeless-shelter error
-    export HOME=$(mktemp -d)
-
-    # To avoid API incompatibilities, these should ideally show the same version
-    echo "> samtools --version"
-    samtools --version
-    echo "> htsfile --version"
-    htsfile --version
-    echo "> bcftools --version"
-    bcftools --version
-
-    # Create auxiliary test data
+  preCheck = ''
+    export HOME=$TMPDIR
     make -C tests/pysam_data
     make -C tests/cbcf_data
-
-    # Delete pysam folder in current directory to avoid importing it during testing
+    make -C tests/tabix_data
     rm -rf pysam
-
-    # Deselect tests that are known to fail due to upstream issues
-    # See https://github.com/pysam-developers/pysam/issues/961
-    py.test \
-      --deselect tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works \
-      --deselect tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected \
-      --deselect tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works \
-      --deselect tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected \
-      --deselect tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile \
-      --deselect tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader \
-      --deselect tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader \
-      --deselect tests/AlignmentFile_test.py::TestIO::testBAM2BAM \
-      --deselect tests/AlignmentFile_test.py::TestIO::testBAM2CRAM \
-      --deselect tests/AlignmentFile_test.py::TestIO::testBAM2SAM \
-      --deselect tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject \
-      --deselect tests/AlignmentFile_test.py::TestIO::testOpenFromFilename \
-      --deselect tests/AlignmentFile_test.py::TestIO::testSAM2BAM \
-      --deselect tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile \
-      --deselect tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate \
-      --deselect tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing \
-      --deselect tests/compile_test.py::BAMTest::testCount \
-      tests/
   '';
 
   pythonImportsCheck = [