Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix bugs finding paths of dependencies #4

Merged
merged 1 commit into from
Feb 17, 2015
Merged

Fix bugs finding paths of dependencies #4

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
39 changes: 22 additions & 17 deletions ariba/external_progs.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,49 +14,52 @@ def is_in_path(prog):


prog_to_version_cmd = {
'bcftools': ('bcftools', re.compile('^Version: ([0-9\.]+)')),
'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version ([0-9\.]+)')),
'smalt': ('smalt version', re.compile('^Version: ([0-9\.]+)')),
'spades': ('spades.py', re.compile('^SPAdes genome assembler v.([0-9\.]+)')),
'samtools': ('samtools', re.compile('^Version: ([0-9\.]+)')),
'sspace': (None, re.compile('^Usage: .*pl \[SSPACE_(.*)\]')),
'gapfiller': (None, re.compile('^Usage: .*pl \[GapFiller_(.*)\]')),
'velvetg': ('velvetg', re.compile('Version ([0-9\.]+)')),
'velveth': ('velveth', re.compile('Version ([0-9\.]+)')),
'bcftools': ('', re.compile('^Version: ([0-9\.]+)')),
'nucmer': ('--version', re.compile('^NUCmer \(NUCleotide MUMmer\) version ([0-9\.]+)')),
'smalt': ('version', re.compile('^Version: ([0-9\.]+)')),
'spades': ('', re.compile('^SPAdes genome assembler v.([0-9\.]+)')),
'samtools': ('', re.compile('^Version: ([0-9\.]+)')),
'sspace': ('', re.compile('^Usage: .*pl \[SSPACE_(.*)\]')),
'gapfiller': ('', re.compile('^Usage: .*pl \[GapFiller_(.*)\]')),
'velvetg': ('', re.compile('Version ([0-9\.]+)')),
'velveth': ('', re.compile('Version ([0-9\.]+)')),
}


def get_version(prog, path=None):
assert prog in prog_to_version_cmd
if path is None:
path = prog

if not is_in_path(path):
raise Error('Error getting version of ' + path + ' - not found in path.')

path = shutil.which(path)

if prog in ['sspace', 'gapfiller']:
cmd = 'perl ' + os.path.realpath(shutil.which(path))
regex = prog_to_version_cmd[prog][1]
else:
cmd, regex = prog_to_version_cmd[prog]
cmd = path + ' ' + cmd

cmd_output = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
cmd_output = common.decode(cmd_output[0]).split('\n')[:-1] + common.decode(cmd_output[1]).split('\n')[:-1]
for line in cmd_output:
hits = regex.search(line)
if hits:
return hits.group(1)
return 'UNKNOWN ...\n I tried running this to get the version: "' + cmd + '"\n and the output didn\'t match this regular expression: "' + regex.pattern + '"'

return hits.group(1), path
return 'UNKNOWN ...\n I tried running this to get the version: "' + cmd + '"\n and the output didn\'t match this regular expression: "' + regex.pattern + '"', path


def check_versions(opts, verbose=False):
if verbose:
print('{:_^79}'.format(' Checking dependencies and their versions '))
print('tool', 'path', 'version', sep='\t')
print('tool', 'version', 'path', sep='\t')

l = [
('bcftools', opts.bcftools),
('nucmer', None),
('nucmer', 'nucmer'),
('smalt', opts.smalt),
('samtools', opts.samtools),
('sspace', opts.sspace),
Expand Down Expand Up @@ -84,16 +87,18 @@ def check_versions(opts, verbose=False):
errors = []

for t in l:
version = get_version(t[0], path=t[1])
version, path = get_version(t[0], path=t[1])
if verbose:
print(t[0], t[1], version, sep='\t')
print(t[0], version, path, sep='\t')

if t[0] in min_versions and LooseVersion(version) < LooseVersion(min_versions[t[0]]):
errors.append(' '.join(['Found version', version, 'of', t[0], 'which is too low! Please update to at least', min_versions[t[0]]]))
errors.append(' '.join(['Found version', version, 'of', t[0], 'which is too low! Please update to at least', min_versions[t[0]] + '\n Found it here:', path]))

if len(errors):
for e in errors:
print('\n*** Error! Bad dependency! ***', file=sys.stderr)
print(e, file=sys.stderr)
print()
raise Error('Cannot continue. Some dependencies need updating')

if verbose:
Expand Down