From 459fc441a3314a073956979ab689533f5c7f71d9 Mon Sep 17 00:00:00 2001 From: Martin Hunt Date: Wed, 18 Feb 2015 15:31:02 +0000 Subject: [PATCH 1/2] Bug fixes with velvet path --- ariba/cluster.py | 5 +++-- ariba/tasks/run.py | 2 ++ 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/ariba/cluster.py b/ariba/cluster.py index 8bd17f89..e47e6288 100644 --- a/ariba/cluster.py +++ b/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 diff --git a/ariba/tasks/run.py b/ariba/tasks/run.py index 7971bc03..1a18c558 100644 --- a/ariba/tasks/run.py +++ b/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] From 11f4c8ab0eef344b60f5253680b19a77790831b7 Mon Sep 17 00:00:00 2001 From: Martin Hunt Date: Wed, 18 Feb 2015 15:31:37 +0000 Subject: [PATCH 2/2] Update version to 0.1.2 --- ariba/common.py | 2 +- setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/ariba/common.py b/ariba/common.py index 7a4170a1..a5004a40 100644 --- a/ariba/common.py +++ b/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: diff --git a/setup.py b/setup.py index 18dab404..b1703354 100644 --- a/setup.py +++ b/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',