Fix cmake clang htslib incompatibility, pt 5

.github/workflows/ci.yaml

@@ -200,7 +200,8 @@ jobs:
 
       - name: Setup C++
         # Reference: https://github.com/marketplace/actions/setup-cpp-c-c
-        uses: aminya/[email protected]
+        # uses: aminya/[email protected]
+        uses: aminya/[email protected]
         if: matrix.compiler != 'apple'
         with:
           compiler: ${{ matrix.compiler }}

tools/cmake/IncludeHtslib.cmake

@@ -194,25 +194,6 @@ if( NOT ( CMAKE_VERSION VERSION_LESS 3.24 ))
     cmake_policy(SET CMP0135 NEW)
 endif()
 
-# We construct the command for configuring htslib here, so that in the ExternalProject_Add call
-# below, we do not have commands with more than one argument. That seems to cause trouble in
-# some weird interaction of cmake, autotools, and clang, and fails in our GitHub Actions builds...
-#
-# We need to manually add -fPIC here, as somehow otherwise the local installation
-# won't link properly. Linking will always remain a mystery to me...
-# Need some special care to fix https://github.com/lczech/grenedalf/issues/12,
-# see https://stackoverflow.com/a/59536947 for the solution.
-SET(
-    HTSLIB_CONFIGURE_COMMAND
-    ./configure CFLAGS=-fPIC CXXFLAGS=-fPIC --prefix=${CMAKE_CURRENT_BINARY_DIR}/genesis-htslib --libdir=${CMAKE_CURRENT_BINARY_DIR}/genesis-htslib/lib --disable-multi-os-directory --disable-libcurl ${HTSLIB_Deflate_configure}
-)
-
-file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/configure-htslib.sh
-"#!/bin/bash" \n
-"cd $(dirname $0)/genesis-htslib-source" \n
-"./configure CFLAGS=-fPIC CXXFLAGS=-fPIC --prefix=${CMAKE_CURRENT_BINARY_DIR}/genesis-htslib --libdir=${CMAKE_CURRENT_BINARY_DIR}/genesis-htslib/lib --disable-multi-os-directory --disable-libcurl ${HTSLIB_Deflate_configure}"
-)
-
 # We download and built on our own, using the correct commit hash to get our exact desired
 # version, and install locally to the build directory.
 ExternalProject_Add(
@@ -242,13 +223,12 @@ ExternalProject_Add(
         # autoheader
         # COMMAND
         # autoconf
-        # COMMAND
-        # For whatever reason, CMake can't make the script executable, so we do that manually...
-        # We tried file(COPY) and simiar, nothing worked :-(
-        COMMAND
-        chmod +x ${CMAKE_CURRENT_BINARY_DIR}/configure-htslib.sh
         COMMAND
-        ${CMAKE_CURRENT_BINARY_DIR}/configure-htslib.sh
+        # We need to manually add -fPIC here, as somehow otherwise the local installation
+        # won't link properly. Linking will always remain a mystery to me...
+        # Need some special care to fix https://github.com/lczech/grenedalf/issues/12,
+        # see https://stackoverflow.com/a/59536947 for the solution.
+        ./configure CFLAGS=-fPIC CXXFLAGS=-fPIC --prefix=${CMAKE_CURRENT_BINARY_DIR}/genesis-htslib --libdir=${CMAKE_CURRENT_BINARY_DIR}/genesis-htslib/lib --disable-multi-os-directory --disable-libcurl ${HTSLIB_Deflate_configure}
 
     # Build Step
     # BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR}/genesis-htslib