Merge pull request #193 from martinghunt/bowtie2_version_issues

Bowtie2 version issues
sanger-pathogens · Aug 14, 2017 · 2c10cdb · 2c10cdb
2 parents 2a58a26 + 20fe8c1
commit 2c10cdb
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Showing 3 changed files with 4 additions and 3 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -28,7 +28,7 @@ ENV ARIBA_BOWTIE2=$PWD/bowtie2-2.2.9/bowtie2 ARIBA_CDHIT=cdhit-est MPLBACKEND="a
 
 RUN git clone https://github.com/sanger-pathogens/ariba.git \
   && cd ariba \
-  && git checkout v2.10.0 \
+  && git checkout v2.10.1 \
   && python3 setup.py test \
   && python3 setup.py install
 

diff --git a/ariba/mapping.py b/ariba/mapping.py
@@ -1,5 +1,6 @@
 import os
 import sys
+from distutils.version import LooseVersion
 import pysam
 import pyfastaq
 from ariba import common
@@ -82,7 +83,7 @@ def run_bowtie2(
         '-2', reads_rev,
     ]
 
-    if bowtie2_version == '2.3.1':
+    if LooseVersion(bowtie2_version) >= LooseVersion('2.3.1'):
         map_cmd.append('--score-min G,1,10')
 
     if remove_both_unmapped:

diff --git a/setup.py b/setup.py
@@ -55,7 +55,7 @@
 setup(
     ext_modules=[minimap_mod, fermilite_mod, vcfcall_mod],
     name='ariba',
-    version='2.10.0',
+    version='2.10.1',
     description='ARIBA: Antibiotic Resistance Identification By Assembly',
     packages = find_packages(),
     package_data={'ariba': ['test_run_data/*']},