kissplice 2.6.5 (new formula) (#1697)

Kissplice was packaged before the migration to brewsci/bio :
https://github.com/brewsci/homebrew-science/blob/master/Formula/kissplice.rb

Modernize packaging with the current configuration :
- gitlab
- modern cmake
- run sample example as test stage. another possibility is running make test in install

Kissplice depends on bcalm, but uses an internal build that is patched to work with ARM MacOS.
The patch has been submitted to bcalm upstream but in the meantime the current bcalm formula does not build on ARM MacOS.

Added patches to remove compiler path (with shim directory) from bcalm.
These patches are quite ugly but necessary to pass brew audit, and would be needed in thebcalm formula too.

Formula/kissplice.rb

@@ -0,0 +1,52 @@
+class Kissplice < Formula
+  # cite Sacomoto_2012: https://doi.org/10.1186/1471-2105-13-S6-S5
+  desc "Local transcriptome assembler for SNPs, indels and AS events"
+  homepage "https://kissplice.prabi.fr"
+  url "https://gitlab.inria.fr/erable/kissplice.git",
+      tag:      "2.6.5",
+      revision: "00cb99c3b1971866089ef0439526647d328115d0"
+  license "CECILL-2.0"
+
+  depends_on "cmake" => :build
+  depends_on "[email protected]" # Python application but only uses standard packages
+
+  uses_from_macos "zlib"
+
+  def install
+    # Fix the content of 2 template files in bcalm that store the compiler path.
+    # The bcalm git is created by cmake ExternalProject step, clear during PATCH_COMMAND.
+    (buildpath/"empty_settings_file").write "Removed but must be non-empty"
+    (buildpath/"fixed_buildinfo_header").write <<-EOF
+      #define STR_LIBRARY_VERSION     "${gatb-core-version}"
+      #define STR_COMPILATION_DATE    "${gatb-core-date}"
+      #define STR_COMPILATION_FLAGS   "${gatb-core-flags}"
+      #define STR_COMPILER            "c compiler  (${CMAKE_CXX_COMPILER_VERSION})"
+      #define STR_OPERATING_SYSTEM    "${CMAKE_SYSTEM}"
+    EOF
+    inreplace "CMakeLists.txt", "# This is run inside bcalm build dir.", <<-EOF
+      PATCH_COMMAND "${CMAKE_COMMAND}" -E copy #{buildpath}/empty_settings_file
+        gatb-core/gatb-core/thirdparty/hdf5/config/cmake/libhdf5.settings.cmake.in
+        && "${CMAKE_COMMAND}" -E copy #{buildpath}/fixed_buildinfo_header
+        gatb-core/gatb-core/src/gatb/system/api/build_info.hpp.in
+    EOF
+
+    system "cmake", "-S", ".", "-B", "build/", "-DUSE_BUNDLED_BCALM=ON", *std_cmake_args
+    system "cmake", "--build", "build/"
+    system "cmake", "--install", "build/"
+  end
+
+  test do
+    resource "git" do
+      url "https://gitlab.inria.fr/erable/kissplice.git",
+          tag:      "2.6.5",
+          revision: "00cb99c3b1971866089ef0439526647d328115d0"
+    end
+
+    resource("git").stage do
+      # Run sample example from the git data
+      system "#{bin}/kissplice",
+        "-r", "sample_example/mock1.fq", "-r", "sample_example/mock2.fq",
+        "-r", "sample_example/virus1.fq", "-r", "sample_example/virus2.fq"
+    end
+  end
+end