Sascha Steinbiss pushed to branch master at Debian Med / ariba
Commits:
4b898686 by Sascha Steinbiss at 2019-09-26T08:24:34Z
New upstream version 2.14.4+ds
- - - - -
e43d01e5 by Sascha Steinbiss at 2019-09-26T08:24:39Z
Merge tag 'upstream/2.14.4+ds'
Upstream version 2.14.4+ds
- - - - -
42210be4 by Sascha Steinbiss at 2019-09-26T08:40:13Z
new upstream release
- - - - -
5 changed files:
- CHANGELOG.md
- ariba/ref_genes_getter.py
- debian/changelog
- debian/patches/add-testdata.patch
- setup.py
Changes:
=====================================
CHANGELOG.md
=====================================
@@ -1,5 +1,12 @@
# Change Log
+[v2.14.4](https://github.com/sanger-pathogens/ariba/tree/v2.14.4) (2019-09-24)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.14.3...v2.14.4)
+
+**Fixed bugs:**
+
+- ARGannot download fails [\#281](https://github.com/sanger-pathogens/ariba/issues/281)
+
[v2.14.3](https://github.com/sanger-pathogens/ariba/tree/v2.14.3) (2019-08-23)
[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.14.2...v2.14.3)
=====================================
ariba/ref_genes_getter.py
=====================================
@@ -277,13 +277,12 @@ class RefGenesGetter:
except:
raise Error('Error mkdir/chdir ' + tmpdir)
- zipfile = 'arg-annot-database_doc.zip'
- common.download_file('http://www.mediterranee-infection.com/arkotheque/client/ihumed/_depot_arko/articles/304/arg-annot-database_doc.zip', zipfile, max_attempts=self.max_download_attempts, sleep_time=self.sleep_time, verbose=True)
- common.syscall('unzip ' + zipfile)
+ downloadfile = 'arg-annot-database_doc'
+ common.download_file('https://www.mediterranee-infection.com/wp-content/uploads/2019/09/ARG-ANNOT_NT_V6_July2019.txt', downloadfile, max_attempts=self.max_download_attempts, sleep_time=self.sleep_time, verbose=True)
os.chdir(current_dir)
print('Extracted files.')
- genes_file = os.path.join(tmpdir, 'Database Nt Sequences File.txt')
+ genes_file = os.path.join(tmpdir, downloadfile)
final_fasta = outprefix + '.fa'
final_tsv = outprefix + '.tsv'
=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+ariba (2.14.4+ds-1) unstable; urgency=medium
+
+ * New upstream release.
+
+ -- Sascha Steinbiss <satta at debian.org> Thu, 26 Sep 2019 10:32:46 +0200
+
ariba (2.14.3+ds-1) unstable; urgency=medium
* New upstream release.
=====================================
debian/patches/add-testdata.patch
=====================================
@@ -4,7 +4,7 @@ Last-Update: 2019-09-09
--- a/setup.py
+++ b/setup.py
@@ -57,7 +57,43 @@
- version='2.14.3',
+ version='2.14.4',
description='ARIBA: Antibiotic Resistance Identification By Assembly',
packages = find_packages(),
- package_data={'ariba': ['test_run_data/*', 'tb_data/*']},
=====================================
setup.py
=====================================
@@ -55,7 +55,7 @@ vcfcall_mod = Extension(
setup(
ext_modules=[minimap_mod, fermilite_mod, vcfcall_mod],
name='ariba',
- version='2.14.3',
+ version='2.14.4',
description='ARIBA: Antibiotic Resistance Identification By Assembly',
packages = find_packages(),
package_data={'ariba': ['test_run_data/*', 'tb_data/*']},
View it on GitLab: https://salsa.debian.org/med-team/ariba/compare/815a7f5e09a8779b055cddadfaf221c693b5239f...42210be4fb16de13793944d36a77249f36db8c32
--
View it on GitLab: https://salsa.debian.org/med-team/ariba/compare/815a7f5e09a8779b055cddadfaf221c693b5239f...42210be4fb16de13793944d36a77249f36db8c32
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