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Commits on Source (3)
New upstream version 2.14.4+ds
· 4b898686
Sascha Steinbiss
authored
Sep 26, 2019
4b898686
Merge tag 'upstream/2.14.4+ds'
· e43d01e5
Sascha Steinbiss
authored
Sep 26, 2019
Upstream version 2.14.4+ds
e43d01e5
new upstream release
· 42210be4
Sascha Steinbiss
authored
Sep 26, 2019
42210be4
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CHANGELOG.md
View file @
42210be4
# 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
View file @
42210be4
...
...
@@ -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
View file @
42210be4
ariba (2.14.4+ds-1) unstable; urgency=medium
* New upstream release.
-- Sascha Steinbiss <satta@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
View file @
42210be4
...
...
@@ -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
View file @
42210be4
...
...
@@ -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/*
'
]},
...
...