def deploy_denoiser(app, setup_dir):
os.rmdir(app.deploy_dir)
util.copytree(setup_dir, app.deploy_dir)
srcName = 'FlowgramAli_4frame_linux_x86_64'
srcPath = os.path.join(app.deploy_dir, 'FlowgramAlignment')
srcPath = os.path.join(srcPath, srcName)
destName = 'FlowgramAli_4frame'
destPath = os.path.join(app.deploy_dir, 'bin')
destPath = os.path.join(destPath, destName)
rc = util.move_file(srcPath, destPath)
if rc != 0:
return rc
update_denoiser_settings(app.deploy_dir)
baseDir = os.path.join(app.deploy_dir, 'Denoiser')
files = ['denoiser.py', 'preprocess.py', 'denoise_postprocess.py', \
'make_cluster_jobs.py']
for aFile in files:
filePath = os.path.join(baseDir, aFile)
rc = util.make_file_user_executable(filePath)
if rc != 0:
app.log.error('Problem making %s executable.' % filePath)
return 0
def _download(self):
self.log.info('Downloading %s' % self.name)
download_release = True
rc = 1
if self.deploy_type == 'repository':
download_release = False
if download_release:
rc = util.download_file(self.release_location,
self.tmp_dir,
self.release_file_name)
else:
if self.local_repository:
# Copy local repository into tmp_dir.
rc = util.copytree(self.repository_location,
os.path.join(self.tmp_dir,
self.repository_local_name))
else:
if self.repository_type == 'svn':
rc = util.svn_checkout(self.repository_location,
self.tmp_dir,
self.repository_local_name,
self.repository_options)
elif self.repository_type == 'git':
rc = util.git_clone(self.repository_location,
self.tmp_dir,
self.repository_local_name,
self.repository_options)
return rc
def _download(self):
self.log.info('Downloading %s' % self.name)
download_release = True
rc = 1
if self.deploy_type == 'repository':
download_release = False
if download_release:
rc = util.download_file(self.release_location, self.tmp_dir,
self.release_file_name)
else:
if self.local_repository:
# Copy local repository into tmp_dir.
rc = util.copytree(
self.repository_location,
os.path.join(self.tmp_dir, self.repository_local_name))
else:
if self.repository_type == 'svn':
rc = util.svn_checkout(self.repository_location,
self.tmp_dir,
self.repository_local_name,
self.repository_options)
elif self.repository_type == 'git':
rc = util.git_clone(self.repository_location, self.tmp_dir,
self.repository_local_name,
self.repository_options)
return rc
def _copy_dir(self, setup_dir):
self.log.debug('Copying %s to final location.' % self.name)
os.rmdir(self.deploy_dir)
rc = util.copytree(setup_dir, self.deploy_dir)
if rc != 0:
self.log.error('Problem copy directory for %s.' % self.name)
return 1
else:
self.log.info('Successfully copied %s directory.' % self.name)
return 0
def _copy_dir(self, setup_dir):
self.log.debug('Copying %s to final location.' % self.name)
os.rmdir(self.deploy_dir)
rc = util.copytree(setup_dir, self.deploy_dir)
if rc != 0:
self.log.error('Problem copy directory for %s.' % self.name)
return 1
else:
self.log.info('Successfully copied %s directory.' % self.name)
return 0
def deploy_ampliconnoise(app, setup_dir):
rc = util.make_install('ampliconnoise', setup_dir)
if rc != 0:
return rc
# Certain versions of AmpliconNoise have a bad symlink that needs to be
# removed, while other versions do not. We use a try/except structure
# instead of using os.path.exists() because broken symlinks will return
# False.
filePath = os.path.join(setup_dir, 'PyroNoiseM/.#Head10.dat')
try:
os.remove(filePath)
except OSError:
pass
os.rmdir(app.deploy_dir)
return util.copytree(setup_dir, app.deploy_dir)
def deploy_dotur(app, setup_dir):
# a hack to fix headers for gcc 4.3+
richFile = os.path.join(setup_dir, 'richness.h')
fileH = open(richFile, 'r')
fileC = fileH.readlines()
fileH.close()
fileH = open(richFile, 'w')
fileH.write('#include <cstdlib>\n')
for line in fileC:
fileH.write(line)
fileH.close()
otuFile = os.path.join(setup_dir, 'otu.h')
fileH = open(otuFile, 'r')
fileC = fileH.readlines()
fileH.close()
fileH = open(otuFile, 'w')
fileH.write('#include <cstdlib>\n#include <algorithm>\n')
for line in fileC:
fileH.write(line)
fileH.close()
doturFile = os.path.join(setup_dir, 'dotur.C')
fileH = open(doturFile, 'r')
fileC = fileH.readlines()
fileH.close()
fileH = open(doturFile, 'w')
fileH.write('#include <cstring>\n')
for line in fileC:
fileH.write(line)
fileH.close()
srcFile = 'dotur.C'
srcFile = os.path.join(setup_dir, srcFile)
if app.exe_name:
exeFile = app.exe_name
else:
exeFile = 'dotur'
exeFile = os.path.join(setup_dir, exeFile)
rc = util.compile_cpp_file('dotur', setup_dir, srcFile, exeFile)
if rc != 0:
return rc
os.rmdir(app.deploy_dir)
return util.copytree(setup_dir, app.deploy_dir)
def deploy_pyronoise(app, setup_dir):
srcDir = os.path.join(setup_dir, 'FDist')
rc = util.make('pyronoise2/FDist', srcDir)
if rc != 0:
return rc
srcDir = os.path.join(setup_dir, 'FastaUnique')
rc = util.make('pyronoise2/FastaUnique', srcDir)
if rc != 0:
return rc
srcDir = os.path.join(setup_dir, 'NDist')
rc = util.make('pyronoise2/NDist', srcDir)
if rc != 0:
return rc
srcDir = os.path.join(setup_dir, 'PCluster')
rc = util.make('pyronoise2/PCluster', srcDir)
if rc != 0:
return rc
srcDir = os.path.join(setup_dir, 'QCluster')
rc = util.make('pyronoise2/QCluster', srcDir)
if rc != 0:
return rc
os.rmdir(app.deploy_dir)
return util.copytree(setup_dir, app.deploy_dir)
