[med-svn] [ariba] 02/02: New upstream version 2.9.2+ds
Sascha Steinbiss
satta at debian.org
Thu Apr 27 08:15:25 UTC 2017
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch upstream
in repository ariba.
commit a3fddfdbab4f6acdf9905d1bbeec7a677f9d9589
Author: Sascha Steinbiss <satta at debian.org>
Date: Thu Apr 27 10:00:54 2017 +0200
New upstream version 2.9.2+ds
---
README.md | 22 +++++++++++++---------
ariba/assembly.py | 1 +
ariba/cluster.py | 1 +
ariba/clusters.py | 2 --
ariba/external_progs.py | 7 +++++++
ariba/mapping.py | 4 ++++
ariba/summary.py | 1 +
ariba/tests/mapping_test.py | 3 +++
install_dependencies.sh | 10 +++++-----
setup.py | 2 +-
10 files changed, 36 insertions(+), 17 deletions(-)
diff --git a/README.md b/README.md
index d67ab84..3b68744 100644
--- a/README.md
+++ b/README.md
@@ -1,16 +1,10 @@
-Disclaimer
-==========
-
-This is pre-publication software that is currently under active development.
-Use it at your own risk. Bug reports are welcome, but
-user support is not provided at this time.
-
-
ARIBA
=====
Antimicrobial Resistance Identification By Assembly
+For methods and benchmarking, please see the [preprint on biorxiv][ariba biorxiv].
+
For how to use ARIBA, please see the [ARIBA wiki page][ARIBA wiki].
@@ -61,6 +55,16 @@ ARIBA is available in the latest version of Debian, and over time will progressi
sudo apt-get install ariba
+### Ubuntu
+
+You can use `apt-get` (see above), or to ensure you get the latest version of ARIBA, the following commands can be
+used to install ARIBA and its dependencies. This was tested on a new instance of Ubuntu 16.04.
+
+ sudo apt-get update
+ sudo apt-get install -y python3-dev python3-pip python3-tk zlib1g-dev bowtie2 mummer cd-hit
+ export ARIBA_CDHIT=cdhit-est
+ sudo pip3 install ariba
+
### Dependencies and environment variables
By default, ARIBA will look for the dependencies in your `$PATH`, using
@@ -135,7 +139,7 @@ Please read the [ARIBA wiki page][ARIBA wiki] for usage instructions.
Build status: [](https://travis-ci.org/sanger-pathogens/ariba)
-
+ [ariba biorxiv]: http://biorxiv.org/content/early/2017/04/07/118000
[bowtie2]: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
[cdhit]: http://weizhongli-lab.org/cd-hit/
[ARIBA wiki]: https://github.com/sanger-pathogens/ariba/wiki
diff --git a/ariba/assembly.py b/ariba/assembly.py
index 721a932..f028a63 100644
--- a/ariba/assembly.py
+++ b/ariba/assembly.py
@@ -211,6 +211,7 @@ class Assembly:
threads=1,
sort=True,
bowtie2=self.extern_progs.exe('bowtie2'),
+ bowtie2_version=self.extern_progs.version('bowtie2'),
verbose=True,
verbose_filehandle=self.log_fh
)
diff --git a/ariba/cluster.py b/ariba/cluster.py
index 6285513..75d244b 100644
--- a/ariba/cluster.py
+++ b/ariba/cluster.py
@@ -352,6 +352,7 @@ class Cluster:
sort=True,
bowtie2=self.extern_progs.exe('bowtie2'),
bowtie2_preset='very-sensitive-local',
+ bowtie2_version=self.extern_progs.version('bowtie2'),
verbose=True,
verbose_filehandle=self.log_fh
)
diff --git a/ariba/clusters.py b/ariba/clusters.py
index b9c5756..ae50cd5 100644
--- a/ariba/clusters.py
+++ b/ariba/clusters.py
@@ -609,8 +609,6 @@ class Clusters:
print('{:_^79}'.format(' Cleaning files '), flush=True)
self._clean()
- print('self.mlst_profile_file', self.mlst_profile_file)
- print('self.report_file_filtered', self.report_file_filtered)
Clusters._write_mlst_reports(self.mlst_profile_file, self.report_file_filtered, self.mlst_reports_prefix, verbose=self.verbose)
if self.clusters_all_ran_ok and self.verbose:
diff --git a/ariba/external_progs.py b/ariba/external_progs.py
index cb92393..dbbe077 100644
--- a/ariba/external_progs.py
+++ b/ariba/external_progs.py
@@ -38,6 +38,7 @@ class ExternalProgs:
self.progs = {}
self.version_report = []
self.all_deps_ok = True
+ self.versions = {}
if verbose:
print('{:_^79}'.format(' Checking dependencies and their versions '))
@@ -60,9 +61,11 @@ class ExternalProgs:
got_version, version = self._get_version(prog, self.progs[prog])
if got_version:
+ self.versions[prog] = version
if prog in min_versions and LooseVersion(version) < LooseVersion(min_versions[prog]):
errors.append(' '.join(['Found version', version, 'of', prog, 'which is too low! Please update to at least', min_versions[prog] + '. Found it here:', prog_exe]))
else:
+ self.versions[prog] = None
errors.append(version)
version = 'ERROR'
@@ -97,6 +100,10 @@ class ExternalProgs:
return self.progs[prog]
+ def version(self, prog):
+ return self.versions[prog]
+
+
@staticmethod
def _get_exe(prog):
'''Given a program name, return what we expect its exectuable to be called'''
diff --git a/ariba/mapping.py b/ariba/mapping.py
index b0455a2..718c2f5 100644
--- a/ariba/mapping.py
+++ b/ariba/mapping.py
@@ -39,6 +39,7 @@ def run_bowtie2(
sort=False,
bowtie2='bowtie2',
bowtie2_preset='very-sensitive-local',
+ bowtie2_version=None,
verbose=False,
verbose_filehandle=sys.stdout,
remove_both_unmapped=False,
@@ -81,6 +82,9 @@ def run_bowtie2(
'-2', reads_rev,
]
+ if bowtie2_version == '2.3.1':
+ map_cmd.append('--score-min G,1,10')
+
if remove_both_unmapped:
map_cmd.append(r''' | awk ' !(and($2,4)) || !(and($2,8)) ' ''')
diff --git a/ariba/summary.py b/ariba/summary.py
index b98f35e..1d1a71e 100644
--- a/ariba/summary.py
+++ b/ariba/summary.py
@@ -267,6 +267,7 @@ class Summary:
'no': '#fb9a99',
'NA': '#ffffff',
'het': '#fdbf6f',
+ 'yes_multi_het': '#fdbf6f',
'fragmented': '#1f78b4',
'interrupted': '#a6cee3',
'partial': '#fdbf6f',
diff --git a/ariba/tests/mapping_test.py b/ariba/tests/mapping_test.py
index a22bbc8..5f908c2 100644
--- a/ariba/tests/mapping_test.py
+++ b/ariba/tests/mapping_test.py
@@ -55,6 +55,7 @@ class TestMapping(unittest.TestCase):
ref,
out_prefix,
bowtie2=extern_progs.exe('bowtie2'),
+ bowtie2_version=extern_progs.version('bowtie2'),
)
expected = get_sam_columns(os.path.join(data_dir, 'mapping_test_bowtie2_unsorted.bam'))
got = get_sam_columns(out_prefix + '.bam')
@@ -75,6 +76,7 @@ class TestMapping(unittest.TestCase):
ref,
out_prefix,
bowtie2=extern_progs.exe('bowtie2'),
+ bowtie2_version=extern_progs.version('bowtie2'),
remove_both_unmapped=True,
)
expected = get_sam_columns(os.path.join(data_dir, 'mapping_test_bowtie2_remove_both_unmapped_reads.bam'))
@@ -96,6 +98,7 @@ class TestMapping(unittest.TestCase):
out_prefix,
sort=True,
bowtie2=extern_progs.exe('bowtie2'),
+ bowtie2_version=extern_progs.version('bowtie2'),
)
expected = get_sam_columns(os.path.join(data_dir, 'mapping_test_bowtie2_sorted.bam'))
got = get_sam_columns(out_prefix + '.bam')
diff --git a/install_dependencies.sh b/install_dependencies.sh
index 489997e..f8180c3 100755
--- a/install_dependencies.sh
+++ b/install_dependencies.sh
@@ -4,11 +4,11 @@ set -x
start_dir=$(pwd)
-BOWTIE2_VERSION=2.2.8
+BOWTIE2_VERSION=2.3.1
CDHIT_VERSION=4.6.5
MUMMER_VERSION=3.23
-BOWTIE2_DOWNLOAD_URL="http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/${BOWTIE2_VERSION}/bowtie2-${BOWTIE2_VERSION}-linux-x86_64.zip"
+BOWTIE2_DOWNLOAD_URL="http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/${BOWTIE2_VERSION}/bowtie2-${BOWTIE2_VERSION}-legacy-linux-x86_64.zip"
CDHIT_DOWNLOAD_URL="https://github.com/weizhongli/cdhit/archive/V${CDHIT_VERSION}.tar.gz"
MUMMER_DOWNLOAD_URL="http://downloads.sourceforge.net/project/mummer/mummer/${MUMMER_VERSION}/MUMmer${MUMMER_VERSION}.tar.gz"
@@ -36,9 +36,9 @@ download () {
# --------------- bowtie2 ------------------
cd $build_dir
-download $BOWTIE2_DOWNLOAD_URL "bowtie2-${BOWTIE2_VERSION}.zip"
-bowtie2_dir="$build_dir/bowtie2-${BOWTIE2_VERSION}"
-unzip -n bowtie2-${BOWTIE2_VERSION}.zip
+download $BOWTIE2_DOWNLOAD_URL "bowtie2-${BOWTIE2_VERSION}-legacy.zip"
+bowtie2_dir="$build_dir/bowtie2-${BOWTIE2_VERSION}-legacy"
+unzip -n bowtie2-${BOWTIE2_VERSION}-legacy.zip
# --------------- cdhit --------------------
diff --git a/setup.py b/setup.py
index a874476..7c673d0 100644
--- a/setup.py
+++ b/setup.py
@@ -55,7 +55,7 @@ vcfcall_mod = Extension(
setup(
ext_modules=[minimap_mod, fermilite_mod, vcfcall_mod],
name='ariba',
- version='2.9.0',
+ version='2.9.2',
description='ARIBA: Antibiotic Resistance Identification By Assembly',
packages = find_packages(),
package_data={'ariba': ['test_run_data/*']},
--
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