Merge pull request #200 from broadinstitute/ct-various-fixes

cmake -> make in diamond, existence checks in diamond and kraken wrappers
broadinstitute · Jan 20, 2016 · 890227d · 890227d
2 parents c997abd + 3fcf941
commit 890227d
Show file tree

Hide file tree

Showing 2 changed files with 10 additions and 7 deletions.
diff --git a/tools/diamond.py b/tools/diamond.py
@@ -26,7 +26,7 @@ class Diamond(tools.Tool):
 
     def __init__(self, install_methods=None):
         if not install_methods:
-            install_methods = [DownloadAndBuildDiamond(URL, os.path.join(DIAMOND_DIR, 'build', 'diamond'))]
+            install_methods = [DownloadAndBuildDiamond(URL, os.path.join(DIAMOND_DIR, 'bin', 'diamond'))]
         super().__init__(install_methods=install_methods)
 
     def version(self):
@@ -105,14 +105,15 @@ def post_download(self):
         diamond_dir = os.path.join(self.destination_dir, DIAMOND_DIR)
         # We should rather have a way to rename self.download_file in
         # DownloadPackage generically.
-        shutil.move(os.path.join(self.destination_dir, DIAMOND_COMMIT_DIR), diamond_dir)
-        build_dir = os.path.join(diamond_dir, 'build')
-        util.file.mkdir_p(build_dir)
+        if not os.path.exists(diamond_dir):
+            shutil.move(os.path.join(self.destination_dir, DIAMOND_COMMIT_DIR), diamond_dir)
+        build_dir = os.path.join(diamond_dir, 'src')
+        #util.file.mkdir_p(build_dir)
         env = os.environ.copy()
         # The default travis gcc version is 4.6, which is too old to build
         # diamond properly.
         if os.environ.get('TRAVIS') == 'true':
             env['CC'] = 'gcc-4.9'
             env['CXX'] = 'g++-4.9'
-        util.misc.run_and_print(['cmake', '..'], env=env, cwd=build_dir)
+        #util.misc.run_and_print(['cmake', '..'], env=env, cwd=build_dir)
         util.misc.run_and_print(['make'], env=env, cwd=build_dir)
diff --git a/tools/kraken.py b/tools/kraken.py
@@ -74,7 +74,8 @@ def post_download(self):
         env['PATH'] = '{}:{}'.format(os.path.dirname(yaggo_path), env['PATH'])
         jellyfish_dir = os.path.join(self.destination_dir, JELLYFISH_DIR)
 
-        shutil.move(os.path.join(self.destination_dir, JELLYFISH_COMMIT_DIR), jellyfish_dir)
+        if not os.path.exists(jellyfish_dir):
+            shutil.move(os.path.join(self.destination_dir, JELLYFISH_COMMIT_DIR), jellyfish_dir)
 
         install_dir = os.path.join(jellyfish_dir, 'local')
         util.file.replace_in_file(
@@ -159,7 +160,8 @@ def post_download(self):
         env['PATH'] = '{}:{}'.format(os.path.dirname(jellyfish_path), env['PATH'])
         kraken_dir = os.path.join(self.destination_dir, KRAKEN_DIR)
 
-        shutil.move(os.path.join(self.destination_dir, KRAKEN_COMMIT_DIR), kraken_dir)
+        if not os.path.exists(kraken_dir):
+            shutil.move(os.path.join(self.destination_dir, KRAKEN_COMMIT_DIR), kraken_dir)
         libexec_dir = os.path.join(kraken_dir, 'libexec')
         bin_dir = os.path.join(kraken_dir, 'bin')
         util.misc.run_and_print(['./install_kraken.sh', 'libexec'], cwd=kraken_dir, env=env)