Add "install-prerequisites" option to installation script

scripts/install.py

@@ -14,16 +14,82 @@
 forest_url_base = os.path.join(google_cloud_octopus_base, "forests")
 forests = ['germline', 'somatic']
 
+latest_llvm = 'llvm'
+latest_gcc = 'gcc@8'
+
 def get_octopus_version():
     return "0.5.2-beta"
 
 def is_unix():
     system = platform.system()
     return system == "Darwin" or system == "Linux"
 
+def is_osx():
+    return platform.system() == "Darwin"
+
 def download_file(url, file_name):
     urllib.request.urlretrieve(url, file_name)
 
+def git_clone(project):
+    call(['git', 'clone', project])
+
+def get_homebrew_name():
+    if is_osx():
+        return 'homebrew'
+    else:
+        return 'brew'
+
+def download_homebrew():
+    if is_osx():
+        git_clone('https://github.com/mxcl/homebrew.git')
+    else:
+        git_clone('https://github.com/Linuxbrew/brew.git')
+
+def install_homebrew():
+    homebrew = get_homebrew_name()
+    if not os.path.exists(homebrew):
+        download_homebrew()
+    brew_bin = homebrew + '/bin/brew'
+    call([brew_bin, 'update'])
+    return brew_bin
+
+def get_required_prerequisites():
+    result = ['cmake']
+    if is_osx():
+        result.append(latest_llvm)
+    else:
+        result.append(latest_gcc)
+    result += ['boost', 'htslib']
+    return result
+
+def get_brewed_compiler_binaries(homebrew_dir):
+    cellar_dir = os.path.join(homebrew_dir, 'Cellar')
+    if is_osx():
+        llvm_dir = os.path.join(cellar_dir, latest_llvm)
+        llvm_version = os.listdir(llvm_dir)[0]
+        llvm_bin_dir = os.path.join(llvm_dir, os.path.join(llvm_version, 'bin'))
+        return os.path.join(llvm_bin_dir, 'clang'), os.path.join(llvm_bin_dir, 'clang++')
+    else:
+        gcc_dir = os.path.join(cellar_dir, latest_gcc)
+        gcc_version = os.listdir(gcc_dir)[0]
+        gcc_bin_dir = os.path.join(gcc_dir, os.path.join(gcc_version, 'bin'))
+        gcc_bin_name = latest_gcc.replace('@', '-')
+        gxx_bin_name =  gcc_bin_name.replace('cc', '++')
+        return os.path.join(gcc_bin_dir, gcc_bin_name), os.path.join(gcc_bin_dir, gxx_bin_name)
+
+def install_prerequisites(build_dir):
+    brew_bin = install_homebrew()
+    prerequisites = get_required_prerequisites()
+    brew_command = [brew_bin, 'install'] + prerequisites
+    if call(brew_command) == 0:
+        prerequisites_dir = os.path.join(build_dir, get_homebrew_name())
+        cc, cxx = get_brewed_compiler_binaries(prerequisites_dir)
+        binaries = {'cmake': os.path.join(prerequisites_dir, 'bin/cmake'),
+                    'c_compiler': cc, 'cxx_compiler': cxx}
+        return prerequisites_dir, binaries
+    else:
+        return None, None
+
 def download_forests(forest_dir, version):
     if not os.path.exists(forest_dir):
         print("No forest directory found, making one")
@@ -75,13 +141,13 @@ def main(args):
     if not args["keep_cache"] and os.path.exists(cmake_cache_file):
         os.remove(cmake_cache_file)
 
+    prerequisites_dir, prerequisites_binaries = None, None
+    if args["install_prerequisites"]:
+        prerequisites_dir, prerequisites_binaries = install_prerequisites(octopus_build_dir)
+
     cmake_options = []
     if args["prefix"]:
         cmake_options.append("-DCMAKE_INSTALL_PREFIX=" + args["prefix"])
-    if args["c_compiler"]:
-        cmake_options.append("-DCMAKE_C_COMPILER=" + args["c_compiler"])
-    if args["cxx_compiler"]:
-        cmake_options.append("-DCMAKE_CXX_COMPILER=" + args["cxx_compiler"])
     if args["debug"]:
         cmake_options.append("-DCMAKE_BUILD_TYPE=Debug")
     elif args["sanitize"]:
@@ -90,18 +156,51 @@ def main(args):
         cmake_options.append("-DCMAKE_BUILD_TYPE=Release")
     if args["static"]:
         cmake_options.append("-DBUILD_SHARED_LIBS=OFF")
-    if args["boost"]:
-        cmake_options.append("-DBOOST_ROOT=" + args["boost"])
-    if args["htslib"]:
-        cmake_options.append("-DHTSLIB_ROOT=" + args["htslib"])
     if args["verbose"]:
         cmake_options.append("CMAKE_VERBOSE_MAKEFILE:BOOL=ON")
+    if prerequisites_dir is not None:
+        if args["c_compiler"]:
+            cmake_options.append("-DCMAKE_C_COMPILER=" + args["c_compiler"])
+        else:
+            cmake_options.append("-DCMAKE_C_COMPILER=" + prerequisites_binaries["c_compiler"])
+        if args["cxx_compiler"]:
+            cmake_options.append("-DCMAKE_CXX_COMPILER=" + args["cxx_compiler"])
+        else:
+            cmake_options.append("-DCMAKE_CXX_COMPILER=" + prerequisites_binaries["cxx_compiler"])
+        if args["boost"]:
+            cmake_options.append("-DBOOST_ROOT=" + args["boost"])
+            cmake_options.append("-DBoost_NO_BOOST_CMAKE=TRUE")
+            cmake_options.append("-DBoost_NO_SYSTEM_PATHS=TRUE")
+        else:
+            cmake_options.append("-DBOOST_ROOT=" + prerequisites_dir)
+            cmake_options.append("-DBoost_NO_BOOST_CMAKE=TRUE")
+            cmake_options.append("-DBoost_NO_SYSTEM_PATHS=TRUE")
+        if args["htslib"]:
+            cmake_options.append("-DHTSLIB_ROOT=" + args["htslib"])
+            cmake_options.append("-DHTSlib_NO_SYSTEM_PATHS=TRUE")
+        else:
+            cmake_options.append("-DHTSLIB_ROOT=" + prerequisites_dir)
+            cmake_options.append("-DHTSlib_NO_SYSTEM_PATHS=TRUE")
+
+        ret = call([prerequisites_binaries['cmake']] + cmake_options + [".."])
+    else:
+        if args["c_compiler"]:
+            cmake_options.append("-DCMAKE_C_COMPILER=" + args["c_compiler"])
+        if args["cxx_compiler"]:
+            cmake_options.append("-DCMAKE_CXX_COMPILER=" + args["cxx_compiler"])
+        if args["boost"]:
+            cmake_options.append("-DBOOST_ROOT=" + args["boost"])
+            cmake_options.append("-DBoost_NO_BOOST_CMAKE=TRUE")
+            cmake_options.append("-DBoost_NO_SYSTEM_PATHS=TRUE")
+        if args["htslib"]:
+            cmake_options.append("-DHTSLIB_ROOT=" + args["htslib"])
+            cmake_options.append("-DHTSlib_NO_SYSTEM_PATHS=TRUE")
 
-    try:
-        # CMake version 3 is called cmake3 in CentOS (see https://github.com/luntergroup/octopus/issues/37).
-        ret = call(["cmake3"] + cmake_options + [".."])
-    except FileNotFoundError:
-        ret = call(["cmake"] + cmake_options + [".."])
+        try:
+            # CMake version 3 is called cmake3 in CentOS (see https://github.com/luntergroup/octopus/issues/37).
+            ret = call(["cmake3"] + cmake_options + [".."])
+        except FileNotFoundError:
+            ret = call(["cmake"] + cmake_options + [".."])
 
     if ret == 0:
         make_options = []
@@ -129,7 +228,12 @@ def main(args):
                         required=False,
                         type=str,
                         help='Install into given location')
+    parser.add_argument('--install-prerequisites',
+                        default=False,
+                        help='Install all prerequisites locally into build directory',
+                        action='store_true')
     parser.add_argument('--clean',
+                        default=False,
                         help='Do a clean install',
                         action='store_true')
     parser.add_argument('-c', '--c_compiler',
@@ -141,15 +245,19 @@ def main(args):
                         type=str,
                         help='C++ compiler path to use')
     parser.add_argument('--keep_cache',
+                        default=False,
                         help='Do not refresh CMake cache',
                         action='store_true')
     parser.add_argument('--debug',
+                        default=False,
                         help='Builds in debug mode',
                         action='store_true')
     parser.add_argument('--sanitize',
+                        default=False,
                         help='Builds in release mode with sanitize flags',
                         action='store_true')
     parser.add_argument('--static',
+                        default=False,
                         help='Builds using static libraries',
                         action='store_true')
     parser.add_argument('--threads',
@@ -164,10 +272,11 @@ def main(args):
                         type=str,
                         help='The HTSlib library root')
     parser.add_argument('--download',
-                        required=False,
-                        help='Try to download octopus classifiers',
+                        default=False,
+                        help='Try to download pre-trained random forests for filtering',
                         action='store_true')
     parser.add_argument('--verbose',
+                        default=False,
                         help='Ouput verbose make information',
                         action='store_true')
     args = vars(parser.parse_args())