def install(self):
"""
Prepare the pipeline.
"""
# Create directory
dest = self.options['location']
if not os.path.exists(dest):
os.mkdir(dest)
prepare.main(self.options, self.buildout)
return dest
def install(self):
"""
Prepare the pipeline.
"""
# Create directory
dest = self.options['location']
if not os.path.exists(dest):
os.mkdir(dest)
prepare.main(self.options, self.buildout)
return dest
def test_main(self):
"""
Test the main method
"""
os.chdir(PATH)
if os.path.exists('src/fastqc'):
os.remove('src/fastqc')
os.makedirs('src/fastqc')
fastqc = open('src/fastqc/fastqc', 'w')
perl_code = ('#!/soft/bin/perl', 'use warnings;')
fastqc.write('\n'.join(perl_code))
fastqc.close()
if os.path.exists('src/pipeline/bin'):
os.removedirs('src/pipeline/bin')
os.makedirs('src/pipeline/bin')
overlap_path = os.path.join(PATH, 'overlap')
overlap = open(overlap_path, 'w')
overlap.write('dummy')
overlap.close()
buildout = BUILDOUT.copy()
buildout['settings'] = {'perl': '/soft/bin/perl',
'overlap': overlap_path,
'gem_folder': PATH,
'nextgem_folder': PATH}
result = main(OPTIONS.copy(), buildout)
self.failUnless(result is None)
