Merge pull request #9 from martinghunt/master

Bux fixes velvet path

ariba/cluster.py

@@ -90,8 +90,9 @@ def __init__(self,
             raise Error('Error! ' + sspace_exe + ' not found in path')
         self.sspace_exe = os.path.realpath(self.sspace_exe) # otherwise sspace dies loading packages
 
-        self.velveth = velvet_exe + 'h'
-        self.velvetg = velvet_exe + 'g'
+        if self.assembler == 'velvet':
+            self.velveth = velvet_exe + 'h'
+            self.velvetg = velvet_exe + 'g'
 
         self.sspace_k = sspace_k
         self.reads_insert = reads_insert

ariba/common.py

@@ -1,7 +1,7 @@
 import sys
 import subprocess
 
-version = '0.1.1'
+version = '0.1.2'
 
 def syscall(cmd, allow_fail=False, verbose=False):
     if verbose:

ariba/tasks/run.py

@@ -49,6 +49,8 @@ def run():
     executables_group.add_argument('--velveth', help=argparse.SUPPRESS)
 
     options = parser.parse_args()
+    if options.assembler == 'velvet':
+        options.velvet = 'velvet'
     ariba.external_progs.check_versions(options, verbose=options.verbose)
     pyfastaq.sequences.codon2aa = pyfastaq.genetic_codes.codes[options.genetic_code]
 

setup.py

@@ -7,7 +7,7 @@
 
 setup(
     name='ariba',
-    version='0.1.1',
+    version='0.1.2',
     description='ARIBA: Antibiotic Resistance Identification By Assembly',
     packages = find_packages(),
     author='Martin Hunt',