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Bowtie2 version issues #193

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merged 2 commits into from
Aug 14, 2017
Merged

Bowtie2 version issues #193

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947e5dc
Change mapping options bor bowtie 2.3.1 and later
martinghunt Aug 14, 2017
20fe8c1
Version bump 2.10.1
martinghunt Aug 14, 2017
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2 changes: 1 addition & 1 deletion Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -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

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3 changes: 2 additions & 1 deletion ariba/mapping.py
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@@ -1,5 +1,6 @@
import os
import sys
from distutils.version import LooseVersion
import pysam
import pyfastaq
from ariba import common
Expand Down Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -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/*']},
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