diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index b63f8ce79..25135fd3e 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -27,7 +27,7 @@ jobs:
         cuda: '11.8.0'
     - name: Install dependencies from apt
       if: matrix.os == 'ubuntu-20.04'
-      run: sudo apt-get update && sudo apt-get install -y --no-install-recommends libhdf5-dev libssl-dev libzstd-dev autoconf && sudo apt-get remove -y libdeflate-dev
+      run: sudo apt-get update && sudo apt-get install -y --no-install-recommends libhdf5-dev libssl-dev libzstd-dev autoconf
     - name: Set up Windows path
       uses: myci-actions/export-env-var-powershell@1
       if: matrix.os == 'windows-2019-large'
diff --git a/cmake/Htslib.cmake b/cmake/Htslib.cmake
index caabc1a39..9260ac2d4 100644
--- a/cmake/Htslib.cmake
+++ b/cmake/Htslib.cmake
@@ -45,7 +45,7 @@ if(NOT TARGET htslib) # lazy include guard
                 BUILD_IN_SOURCE 1
                 CONFIGURE_COMMAND ${AUTOHEADER_COMMAND}
                 COMMAND ${AUTOCONF_COMMAND}
-                COMMAND ./configure --disable-bz2 --disable-lzma --disable-libcurl --disable-s3 --disable-gcs ${CONFIGURE_FLAGS}
+                COMMAND ./configure --disable-bz2 --disable-lzma --disable-libcurl --disable-s3 --disable-gcs --without-libdeflate ${CONFIGURE_FLAGS}
                 BUILD_COMMAND ${MAKE_COMMAND} install prefix=${htslib_PREFIX}
                 COMMAND ${INSTALL_NAME}
                 INSTALL_COMMAND ""