installing bowtie2 on setup. not debugged

magellan/requirements.txt

@@ -1,2 +1,3 @@
 pandas >= 0.18.0
 numpy >= 1.11.1
+pysam == 0.13

magellan/setup.py

@@ -1,11 +1,134 @@
 import os
 import sys
 from setuptools import setup, Command
+from setuptools.command.install import install
+import zipfile
+import subprocess
 
+try:
+    from urllib.request import urlretrieve
+except ImportError:
+    from urllib import urlretrieve
 
 _python = 'python%d' % sys.version_info.major
 
 
+def find_install(software_name):
+    '''
+    Check if software is installed.
+    '''
+    try:
+        software_path = subprocess.Popen(['which', software_name], stdout=subprocess.PIPE).communicate()[0].decode()
+        if len(software_path) == 0:
+            return None
+        if not os.access(software_path, os.X_OK):
+            return None
+        print 'Found software at: ' + software_path
+        return software_path
+    except Exception:
+        return None
+
+
+def find_exe_in_path(software_name):
+    """
+    Check that an executable exists in $PATH
+    """
+
+    paths = os.environ["PATH"].split(os.pathsep)
+    for path in paths:
+        check_exe_full_path = os.path.join(path, software_name)
+        if os.path.exists(check_exe_full_path):
+            if os.access(check_exe_full_path, os.X_OK):
+                return path
+    return None
+
+
+def download_unpack_zip(url, dest_folder, filename, software_name):
+    """
+    Download the url to the file and decompress into the folder
+    """
+
+    # Check for write permission to the target folder
+    if not os.access(dest_folder, os.W_OK):
+        print 'WARNING: Destination directory is not writeable: ' + dest_folder
+
+    print 'downloading ' + url
+    urlretrieve(url, os.path.join(dest_folder, filename))
+
+    try:
+        zipfile_handle = zipfile.ZipFile(os.path.join(dest_folder, filename))
+        zipfile_handle.extractall(path=dest_folder)
+        zipfile_handle.close()
+        return True
+    except EnvironmentError:
+        print 'WARNING: Unable to extract ' + software_name
+        return False
+
+
+def install_bowtie2(base_folder=None, mac_os=False):
+    """
+    Download and install the bowtie2 software if not already installed. Based on HumanN code at:
+    https://bitbucket.org/biobakery/humann2/src/76e92a1250f0265dff390ba903ba22b8a74b6c8e/setup.py?at=default&fileviewer=file-view-default
+    """
+
+    bowtie2_exe = 'bowtie2'
+    # Check if bowtie2 is already installed
+    bowtie2_path = find_install(bowtie2_exe)  # find_exe_in_path(bowtie2_exe)
+
+    if not bowtie2_path:
+        bowtie2_url = 'https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.4.3/bowtie2-2.3.4.3-linux-x86_64.zip/download'
+        if mac_os:
+            bowtie2_url = 'https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.4.3/bowtie2-2.3.4.3-macos-x86_64.zip/download'
+
+        if not base_folder:
+            base_folder = os.getcwd()
+        bowtie2_install_folder = os.path.join(base_folder, 'bowtie2-2.3.4.3')
+        bowtie2_download_file = os.path.split(os.path.split(bowtie2_url)[0])[1]
+        print 'DEBUG: Did not find BOWTIE2, This is found url - ' + bowtie2_url + '. This is download dir - ' + bowtie2_install_folder
+
+        os.mkdir(bowtie2_install_folder)
+
+        # install the bowtie2 software
+        print('Bowtie2 missing, installing')
+        install_error = False
+        exe_dir = os.path.join(bowtie2_install_folder, os.path.splitext(bowtie2_download_file)[0])
+        print 'This is the expected exe dir ' + exe_dir
+
+        download_ok = download_unpack_zip(bowtie2_url, bowtie2_install_folder, bowtie2_download_file, bowtie2_exe)
+
+        if not download_ok:
+            install_error = True
+        else:
+            #os.environ["PATH"] += os.pathsep + exe_dir
+
+            files = []
+            try:
+                files = os.listdir(exe_dir)
+                if bowtie2_exe not in files:
+                    raise EnvironmentError('Bowtie2 exe not found')
+            except EnvironmentError:
+                print("WARNING: Bowtie2 files not found.")
+                install_error = True
+
+        if install_error:
+            print 'WARNING: Unable to install bowtie2.'
+        else:
+            print 'Installed bowtie2 at ' + exe_dir
+
+    else:
+        print 'Found bowtie2 at ' + bowtie2_path
+
+
+class _InstallCommand(install):
+    def run(self):
+        # find out the platform
+        mac_os = False
+        if sys.platform in ['darwin', 'os2', 'os2emx']:
+            mac_os = True
+        install_bowtie2(mac_os=mac_os)
+        install.run(self)
+
+
 class _TestCommand(Command):
     user_options = [
         ]
@@ -39,6 +162,7 @@ def run(self):
     include_package_data=True,
     cmdclass={
         'test': _TestCommand,
+        'install': _InstallCommand
     },
     classifiers=[
         'Development Status :: 4 - Beta',