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Progcheck report full paths #37

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merged 3 commits into from
Sep 1, 2015
Merged

Progcheck report full paths #37

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b98f0c6
Report full path to binaries
Sep 1, 2015
6fd8170
Stop if any program not found
Sep 1, 2015
0439b28
Version bump 1.0.1
Sep 1, 2015
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2 changes: 1 addition & 1 deletion circlator/common.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@

class Error (Exception): pass

version = '1.0.0'
version = '1.0.1'

def syscall(cmd, allow_fail=False, verbose=False):
if verbose:
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4 changes: 2 additions & 2 deletions circlator/external_progs.py
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Expand Up @@ -85,10 +85,10 @@ def make_and_check_prog(name, verbose=False, raise_error=True, filehandle=None):
return p

if verbose:
print('Using', name, 'version', p.version())
print('Using', name, 'version', p.version(), 'as', p.full_path)

if filehandle:
print('Using', name, 'version', p.version(), file=filehandle)
print('Using', name, 'version', p.version(), 'as', p.full_path, file=filehandle)

return p

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3 changes: 2 additions & 1 deletion circlator/program.py
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Expand Up @@ -17,6 +17,7 @@ def __init__(self, name, version_cmd, version_regex, environment_var=None):

self.version_cmd = version_cmd
self.version_regex = version_regex
self.full_path = shutil.which(self.path)


def in_path(self):
Expand All @@ -43,7 +44,7 @@ def version_at_least(self, min_version):
v = self.version()
if v is None:
return None
return LooseVersion(v) >= LooseVersion(min_version)
return LooseVersion(v) >= LooseVersion(min_version)


def exe(self):
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4 changes: 2 additions & 2 deletions circlator/tasks/all.py
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Expand Up @@ -60,7 +60,7 @@ def run():
options = parser.parse_args()

print_message('{:_^79}'.format(' Checking external programs '), options)
circlator.external_progs.check_all_progs(verbose=options.verbose)
circlator.external_progs.check_all_progs(verbose=options.verbose, raise_error=True)

files_to_check = [options.assembly, options.reads]
if options.b2r_only_contigs:
Expand Down Expand Up @@ -89,7 +89,7 @@ def run():

with open('00.info.txt', 'w') as f:
print(sys.argv[0], 'all', ' '.join(sys.argv[1:]), file=f)
circlator.external_progs.check_all_progs(filehandle=f)
circlator.external_progs.check_all_progs(filehandle=f, raise_error=True)

original_assembly_renamed = '00.input_assembly.fasta'
bam = '01.mapreads.bam'
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2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -7,7 +7,7 @@

setup(
name='circlator',
version='1.0.0',
version='1.0.1',
description='circlator: a tool to circularise genome assemblies',
packages = find_packages(),
package_data={'circlator': ['data/*']},
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