add post-install command for conda installs (#340)

add post-install command for conda installs; use this to copy in
novoalign license if NOVOALIGN_LICENSE_PATH is specified

tools/__init__.py

@@ -215,6 +215,8 @@ def __init__(
         env_root_path=None,
         conda_cache_path=None,
         patches=None,
+        post_install_command=None,
+        post_install_ret=0
     ):
         # if the executable name is specifed, use it; otherwise use the package name
         self.executable = executable or package
@@ -225,6 +227,9 @@ def __init__(
         else:
             self.version = CondaPackageVersion(version)
 
+        self.post_install_command = post_install_command
+        self.post_install_ret = post_install_ret
+
         self.verifycmd = verifycmd
         self.verifycode = verifycode
         self.require_executability = require_executability
@@ -411,6 +416,7 @@ def _attempt_install(self):
         _log.debug("Attempting install...")
         self.install_package()
         self.verify_install()
+        self.post_install()
 
     def get_installed_version(self):
         # If we ever use conda to install pip packages as tools, "-c" needs to be removed
@@ -537,6 +543,17 @@ def install_package(self):
                 # we were able to create the environment and install the package
                 _log.debug("Conda environment created and package installed.")
 
+    def post_install(self):
+        """
+            Runs a shell command after package installation, 
+            relative to the directory containing the executable
+        """
+        if self.post_install_command:
+            destination_dir = os.path.dirname(os.path.realpath(self.executable_path()))
+            return_code = os.system('cd "{}" && {}'.format(destination_dir, self.post_install_command))
+            if self.post_install_ret is not None:
+                assert return_code == self.post_install_ret
+
 
 class DownloadPackage(InstallMethod):
     ''' This is an install method for downloading, unpacking, and post-

tools/novoalign.py

@@ -39,7 +39,10 @@ def __init__(self, path=None):
                         require_executability=True
                     )
                 )
-        install_methods.append(tools.CondaPackage(TOOL_NAME, version=TOOL_VERSION))
+        if os.environ.get("NOVOALIGN_LICENSE_PATH"):
+            install_methods.append(tools.CondaPackage(TOOL_NAME, version=TOOL_VERSION, post_install_command="cp $NOVOALIGN_LICENSE_PATH ./"))
+        else:
+            install_methods.append(tools.CondaPackage(TOOL_NAME, version=TOOL_VERSION))
         tools.Tool.__init__(self, install_methods=install_methods)
 
     def version(self):
@@ -50,7 +53,7 @@ def version(self):
     def _get_tool_version(self):
         tmpf = util.file.mkstempfname('.novohelp.txt')
         with open(tmpf, 'wt') as outf:
-            util.misc.run_and_save([self.install_and_get_path()], outf=outf)
+            util.misc.run_and_save([self.install_and_get_path(), "-V"], outf=outf, check=False)
         with open(tmpf, 'rt') as inf:
             self.tool_version = inf.readline().strip().split()[1]
         os.unlink(tmpf)

util/misc.py

@@ -265,7 +265,7 @@ def run_and_print(args, stdout=None, stderr=None,
 
 def run_and_save(args, stdout=None, stdin=None,
                  outf=None, stderr=None, preexec_fn=None,
-                 close_fds=False, shell=False, cwd=None, env=None):
+                 close_fds=False, shell=False, cwd=None, env=None, check=True):
     assert outf is not None
 
     sp = subprocess.Popen(args,
@@ -283,7 +283,7 @@ def run_and_save(args, stdout=None, stdin=None,
     if err:
         sys.stdout.write(err.decode("UTF-8"))
 
-    if sp.returncode != 0:
+    if sp.returncode != 0 and check:
         raise subprocess.CalledProcessError(sp.returncode, str(args[0]))
 
     return sp
@@ -378,4 +378,18 @@ def available_cpu_count():
     except IOError:
         pass
 
-    return multiprocessing.cpu_count()
+    return multiprocessing.cpu_count()
+
+def which(application_binary_name):
+    """
+        Similar to the *nix "which" command, 
+        this function finds the first executable binary present
+        in the system PATH for the binary specified. 
+        It differs in that it resolves symlinks.
+    """
+    path=os.getenv('PATH')
+    for path in path.split(os.path.pathsep):
+        full_path=os.path.join(path, application_binary_name)
+        if os.path.exists(full_path) and os.access(full_path, os.X_OK):
+            link_resolved_path = os.path.realpath(full_path)
+            return link_resolved_path