Merge pull request #287 from broadinstitute/sy-diamond-update

Update diamond conda version to 0.7.10
broadinstitute · May 3, 2016 · 6a76353 · 6a76353
2 parents 5a40596 + 658800c
commit 6a76353
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Showing 3 changed files with 12 additions and 6 deletions.
diff --git a/tools/__init__.py b/tools/__init__.py
@@ -303,7 +303,7 @@ def _patch(self, path, patch):
 
     @property
     def _package_installed(self):
-        result = util.misc.run_and_print(["conda", "list", "-f", "-c", "-p", self.env_path, "--json", self.package], silent=True, check=True, env=self.conda_env)
+        result = util.misc.run_and_print(["conda", "list", "-f", "-c", "-p", self.env_path, "--json", self.package], silent=True, env=self.conda_env)
         if result.returncode == 0:
             command_output = result.stdout.decode("UTF-8")
             data = json.loads(self._string_from_start_of_json(command_output))
@@ -381,7 +381,7 @@ def get_installed_version(self):
         run_cmd = ["conda", "list", "-c", "--json", "-f", "-p", self.env_path, self.package]
 
 
-        result = util.misc.run_and_print(run_cmd, silent=True, check=True, env=self.conda_env)
+        result = util.misc.run_and_print(run_cmd, silent=True, env=self.conda_env)
         if result.returncode == 0:
             try:
                 command_output = result.stdout.decode("UTF-8")
@@ -407,7 +407,6 @@ def uninstall_package(self):
         result = util.misc.run_and_print(
             run_cmd,
             silent=True,
-            check=True,
             env=self.conda_env)
 
         if result.returncode == 0:
@@ -435,7 +434,7 @@ def install_package(self):
             python_version = "python=" + python_version if python_version else ""
             run_cmd.extend([python_version])
 
-        result = util.misc.run_and_print(run_cmd, silent=True, check=True, env=self.conda_env)
+        result = util.misc.run_and_print(run_cmd, silent=True, env=self.conda_env)
         try:
             command_output = result.stdout.decode("UTF-8")
             data = json.loads(self._string_from_start_of_json(command_output))
@@ -454,7 +453,6 @@ def install_package(self):
                     self._package_str
                 ],
                 silent=True,
-                check=True,
                 env=self.conda_env,
             )
 

diff --git a/tools/diamond.py b/tools/diamond.py
@@ -15,6 +15,7 @@
 
 URL = 'https://github.com/bbuchfink/diamond/archive/b576a5c03177603554f4627ae367f7bcbc6b8dcb.zip'
 TOOL_VERSION = '0.7.9'
+CONDA_VERSION = tools.CondaPackageVersion('0.7.10', 'boost1.60_1')
 DIAMOND_COMMIT_DIR = 'diamond-b576a5c03177603554f4627ae367f7bcbc6b8dcb'
 DIAMOND_DIR = 'diamond-{}'.format(TOOL_VERSION)
 
@@ -27,7 +28,9 @@ class Diamond(tools.Tool):
 
     def __init__(self, install_methods=None):
         if not install_methods:
-            install_methods = [DownloadAndBuildDiamond(URL, os.path.join(DIAMOND_DIR, 'bin', 'diamond'))]
+            install_methods = [
+                tools.CondaPackage("diamond", version=CONDA_VERSION),
+                DownloadAndBuildDiamond(URL, os.path.join(DIAMOND_DIR, 'bin', 'diamond'))]
         super().__init__(install_methods=install_methods)
 
     def version(self):

diff --git a/util/misc.py b/util/misc.py
@@ -175,6 +175,7 @@ def run(args, stdin=None, stdout=None, stderr=None, shell=False,
                 error = ''
             if check and returncode != 0:
                 print(output.decode("utf-8"))
+                print(error.decode("utf-8"))
                 try:
                     raise subprocess.CalledProcessError(
                         returncode, args, output, error)
@@ -213,6 +214,10 @@ def run_and_print(args, stdout=None, stderr=None,
                     log.log(loglevel, result.stdout.decode('utf-8'))
                 else:
                     print(e.output.decode('utf-8'))
+                    try:
+                        print(e.stderr.decode('utf-8'))
+                    except TypeError:
+                        pass
                     sys.stdout.flush()
                 raise(e)
         else: