Code

Merge latest ariba code from master#1

Code

Merged

antunderwood merged 160 commits intoantunderwood:masterantunderwood/ariba:masterfrom sanger-pathogens:mastersanger-pathogens/ariba:masterCopy head branch name to clipboardDec 18, 2019

+828,126-354

Commits

Commits on Aug 14, 2017

• Merge pull request #192 from aunderwo/master

  Show description for 2a58a26
  martinghunt

  authored
  2a58a26

  Copy full SHA for 2a58a26

• Change mapping options bor bowtie 2.3.1 and later

  martinghunt

  committed
  947e5dc

  Copy full SHA for 947e5dc

• Version bump 2.10.1

  martinghunt

  committed
  20fe8c1

  Copy full SHA for 20fe8c1

• Merge pull request #193 from martinghunt/bowtie2_version_issues

  Show description for 2c10cdb
  martinghunt

  authored
  2c10cdb

  Copy full SHA for 2c10cdb

• Add curl

  martinghunt

  committed
  47c002b

  Copy full SHA for 47c002b

• Merge pull request #194 from martinghunt/master

  Show description for 0ad71d7
  martinghunt

  authored
  0ad71d7

  Copy full SHA for 0ad71d7

Commits on Aug 30, 2017

• correct spelling mistake

  EdwardBetts

  authored
  ddd748c

  Copy full SHA for ddd748c

• Merge pull request #195 from EdwardBetts/patch-1

  Show description for 54d0686
  andrewjpage

  authored
  54d0686

  Copy full SHA for 54d0686

Commits on Nov 7, 2017

• Changed card to utilise .tar.bz2 from .tar.gz

  

  Jez Swann

  authored and

  Jez Swann

  committed
  eb865f9

  Copy full SHA for eb865f9

Commits on Nov 8, 2017

• Merge pull request #201 from JezSw/hotfix/changeCardToBZ2

  Show description for 8ec70e5
  martinghunt

  authored
  8ec70e5

  Copy full SHA for 8ec70e5

• Version bump 2.10.2

  martinghunt

  committed
  91d5f70

  Copy full SHA for 91d5f70

• Merge pull request #202 from martinghunt/master

  Show description for 15870cf
  martinghunt

  authored
  15870cf

  Copy full SHA for 15870cf

Commits on Nov 24, 2017

• Bug fix, was getting max instead of min het percent

  martinghunt

  committed
  1fd2c63

  Copy full SHA for 1fd2c63

• Version bump 2.10.3

  martinghunt

  committed
  cffb8f8

  Copy full SHA for cffb8f8

• Merge pull request #204 from martinghunt/mlst_hetmin_bug

  Show description for a2e9c4e
  martinghunt

  authored
  a2e9c4e

  Copy full SHA for a2e9c4e

Commits on Jan 12, 2018

• update readme

  

  Sara Sjunnebo

  committed
  f6c7d13

  Copy full SHA for f6c7d13

• Merge pull request #208 from ssjunnebo/574328_fix_readme

  Show description for a76d131
  ssjunnebo

  authored
  a76d131

  Copy full SHA for a76d131

Commits on Feb 1, 2018

• dont require X to run ariba

  andrewjpage

  committed
  4ab0f10

  Copy full SHA for 4ab0f10

• Merge pull request #209 from andrewjpage/master

  Show description for 7c37d31
  andrewjpage

  authored
  7c37d31

  Copy full SHA for 7c37d31

• Option to run subprocess w/o shell

  

  Andrey Tovchigrechko

  committed
  601e86c

  Copy full SHA for 601e86c

• Remove reference to spades options in tests that are not using spades.

  Show description for 4fb0392
  

  Andrey Tovchigrechko

  committed
  4fb0392

  Copy full SHA for 4fb0392

• Reintroduce Spades as another assembly option. Multithreading for Spades and Bowtie2.

  Show description for e86c9c1
  

  Andrey Tovchigrechko

  committed
  e86c9c1

  Copy full SHA for e86c9c1

Commits on Feb 2, 2018

• Merge pull request #210 from andreyto/at_spades

  Show description for 8478708
  martinghunt

  authored
  8478708

  Copy full SHA for 8478708

• Update setup.py

  andrewjpage

  authored
  4d97318

  Copy full SHA for 4d97318

• automatically release to pypi

  andrewjpage

  committed
  958ed64

  Copy full SHA for 958ed64

• Merge branch 'master' of github.com:sanger-pathogens/ariba

  andrewjpage

  committed
  1363dcc

  Copy full SHA for 1363dcc

• remove deploy

  andrewjpage

  committed
  c659946

  Copy full SHA for c659946

Commits on Feb 9, 2018

• fixed card db path

  eppinglen

  committed
  18be23e

  Copy full SHA for 18be23e

• version 2.11.1

  eppinglen

  committed
  1dfb58b

  Copy full SHA for 1dfb58b

Commits on Feb 19, 2018

• card db bz2|gz regex

  eppinglen

  committed
  bfd6cc9

  Copy full SHA for bfd6cc9

Commits on Feb 26, 2018

• Merge pull request #213 from eppinglen/master

  Show description for 379fbb3
  ssjunnebo

  authored
  379fbb3

  Copy full SHA for 379fbb3

Commits on Apr 9, 2018

• change path to license file

  

  Sara Sjunnebo

  committed
  c9af44f

  Copy full SHA for c9af44f

• Merge pull request #219 from ssjunnebo/574328_fix_readme

  Show description for b61b029
  ssjunnebo

  authored
  b61b029

  Copy full SHA for b61b029

Commits on Apr 22, 2018

• Fix nucmer regex to work with 3.1 and 4.0

  martinghunt

  committed
  9949c6a

  Copy full SHA for 9949c6a

• New method _fix_virulencefinder_fasta_file

  martinghunt

  committed
  78cb703

  Copy full SHA for 78cb703

• Fix virulencefinder fasta files, including '>' at end of line

  martinghunt

  committed
  ef5edb3

  Copy full SHA for ef5edb3

Commits on Apr 23, 2018

• Version bump 2.11.2

  martinghunt

  committed
  7b4f782

  Copy full SHA for 7b4f782

• Merge pull request #220 from martinghunt/various_fixes

  Show description for a7cd6a7
  martinghunt

  authored
  a7cd6a7

  Copy full SHA for a7cd6a7

Commits on May 13, 2018

• New method _get_genetic_epi_database_from_bitbucket

  martinghunt

  committed
  5ee343a

  Copy full SHA for 5ee343a

• Get resfinder from bitbucket

  martinghunt

  committed
  4432aff

  Copy full SHA for 4432aff

• Get plasmidfinder and viruslencefinder from bitbucket

  martinghunt

  committed
  5f85c47

  Copy full SHA for 5f85c47

• Merge pull request #222 from martinghunt/getref_xfinder_bitbucket

  Show description for d58db1e
  martinghunt

  authored
  d58db1e

  Copy full SHA for d58db1e

• Get srst2_argannot latest version r2 by default

  martinghunt

  committed
  98ea78b

  Copy full SHA for 98ea78b

• Merge pull request #223 from martinghunt/srst2_argannot_r2

  Show description for f4539a6
  martinghunt

  authored
  f4539a6

  Copy full SHA for f4539a6

• Remove spades warnings. Check spades found if actually using it

  martinghunt

  committed
  039ded6

  Copy full SHA for 039ded6

• Version bump 2.12.0

  martinghunt

  committed
  2038c85

  Copy full SHA for 2038c85

• Merge pull request #224 from martinghunt/remove_spades_warnings

  Show description for 7e0d61a
  martinghunt

  authored
  7e0d61a

  Copy full SHA for 7e0d61a

Commits on May 30, 2018

• Update docker image to Ubuntu 17.10 and Ariba v.2.12.0

  

  Sara Sjunnebo

  committed
  84dd14d

  Copy full SHA for 84dd14d

Commits on May 31, 2018

• Merge pull request #227 from ssjunnebo/625329_Update_Docker

  Show description for 2650a01
  ssjunnebo

  authored
  2650a01

  Copy full SHA for 2650a01

Commits on Jun 15, 2018

• Bug fix virulencefinder was getting plasmidfinder

  martinghunt

  committed
  2b3cdec

  Copy full SHA for 2b3cdec

• Version bump 2.12.1

  martinghunt

  committed
  8cff19e

  Copy full SHA for 8cff19e

• Merge pull request #228 from martinghunt/fix_virulencefinder_download

  Show description for 54f4f9d
  martinghunt

  authored
  54f4f9d

  Copy full SHA for 54f4f9d

Commits on Jul 13, 2018

• Set theme jekyll-theme-cayman

  ssjunnebo

  committed
  7d9bef7

  Copy full SHA for 7d9bef7

Commits on Jul 16, 2018

• Include conda and docker badges

  

  Sara Sjunnebo

  committed
  6763008

  Copy full SHA for 6763008

• Merge pull request #233 from ssjunnebo/621556_badges

  Show description for 1efdcc7
  ssjunnebo

  authored
  1efdcc7

  Copy full SHA for 1efdcc7

Commits on Aug 9, 2018

• Add to codecov

  

  Sara Sjunnebo

  committed
  796e6f3

  Copy full SHA for 796e6f3

• Merge pull request #234 from ssjunnebo/627258_codecov

  Show description for 1deda7a
  ssjunnebo

  authored
  1deda7a

  Copy full SHA for 1deda7a

Commits on Aug 10, 2018

• New function rmtree

  martinghunt

  committed
  294fdef

  Copy full SHA for 294fdef

• Use rm -rf everywhere instead of shutil.rmtree

  martinghunt

  committed
  8c0ca1f

  Copy full SHA for 8c0ca1f

• Merge pull request #235 from martinghunt/do_not_use_rmtree

  Show description for cf8e126
  martinghunt

  authored
  cf8e126

  Copy full SHA for cf8e126

Commits on Sep 11, 2018

• Updating NCBI download feature

  schultzm

  committed
  95a22dd

  Copy full SHA for 95a22dd

• Almost working NCBI

  schultzm

  committed
  76c8c79

  Copy full SHA for 76c8c79

Commits on Sep 13, 2018

• Working version of ncbi download and use

  schultzm

  committed
  78949bf

  Copy full SHA for 78949bf

• ncbi download workds

  schultzm

  committed
  d065240

  Copy full SHA for d065240

• Took out the garbage

  schultzm

  committed
  6561f0f

  Copy full SHA for 6561f0f

Commits on Sep 14, 2018

• updated .travis.yml to use python3.6

  schultzm

  committed
  be4dbf7

  Copy full SHA for be4dbf7

Commits on Oct 23, 2018

• Fixed bug in fermilite path

  schultzm

  committed
  111a31a

  Copy full SHA for 111a31a

Commits on Nov 1, 2018

• New module tb and function report_to_resistance_dict

  martinghunt

  committed
  149ba04

  Copy full SHA for 149ba04

• New method _write_tb_resistance_calls_json

  martinghunt

  committed
  d8c8b3b

  Copy full SHA for d8c8b3b

• Add option to load arbitrary parameters from JSON file

  martinghunt

  committed
  4ddcdf4

  Copy full SHA for 4ddcdf4

• Load extra parameters file (if present)

  martinghunt

  committed
  941a944

  Copy full SHA for 941a944

Commits on Nov 6, 2018

• Call tb resistance if in params JSON file

  martinghunt

  committed
  cf5d253

  Copy full SHA for cf5d253

Commits on Nov 15, 2018

• New function genbank_to_gene_coords

  martinghunt

  committed
  d54a502

  Copy full SHA for d54a502

• New function load_mutations

  martinghunt

  committed
  4f635c7

  Copy full SHA for 4f635c7

• Add TB reference NC_000962.3 genome

  martinghunt

  committed
  ef5ac16

  Copy full SHA for ef5ac16

• New function write_prepareref_fasta_file

  martinghunt

  committed
  1fb8e21

  Copy full SHA for 1fb8e21

• New function write_prepareref_metadata_file

  martinghunt

  committed
  8665afa

  Copy full SHA for 8665afa

• Add tb variant panel files

  martinghunt

  committed
  ae1bf70

  Copy full SHA for ae1bf70

• New function make_prepareref_files

  martinghunt

  committed
  0eeba81

  Copy full SHA for 0eeba81

• Replace upstream variant with original mutation

  martinghunt

  committed
  70b1551

  Copy full SHA for 70b1551

• New function make_prepareref_dir

  martinghunt

  committed
  3c20069

  Copy full SHA for 3c20069

• New task prepareref_tb

  martinghunt

  committed
  4f01ac2

  Copy full SHA for 4f01ac2

Commits on Nov 16, 2018

• bug fix getting drug name from report.tsv

  martinghunt

  committed
  e34d7ec

  Copy full SHA for e34d7ec

• Use python 3.5 instead of 3.4 to stop matplotlib errors

  martinghunt

  committed
  32d1969

  Copy full SHA for 32d1969

• Merge pull request #242 from martinghunt/tb_amr

  Show description for dc378cf
  martinghunt

  authored
  dc378cf

  Copy full SHA for dc378cf

• Fix linebreaks in resfinder fastas

  martinghunt

  committed
  12e9713

  Copy full SHA for 12e9713

• Version bump 2.13.0

  martinghunt

  committed
  9cdb1ed

  Copy full SHA for 9cdb1ed

• Merge pull request #243 from martinghunt/resfinder_linebreaks

  Show description for f0ccf42
  martinghunt

  authored
  f0ccf42

  Copy full SHA for f0ccf42

• Include tb_data dir in release

  martinghunt

  committed
  f328689

  Copy full SHA for f328689

• Merge pull request #244 from martinghunt/master

  Show description for 943f525
  martinghunt

  authored
  943f525

  Copy full SHA for 943f525

Commits on Dec 3, 2018

• Addition of ariba/tb.py itroduced biopython as dependency. Need python >= 3.4 for this.

  

  Sara Sjunnebo

  committed
  e210456

  Copy full SHA for e210456

• Merge pull request #247 from ssjunnebo/update_python_version

  Show description for 82a64f6
  ssjunnebo

  authored
  82a64f6

  Copy full SHA for 82a64f6

Commits on Dec 4, 2018

• Added changelog

  

  Sara Sjunnebo

  committed
  fb0ebe8

  Copy full SHA for fb0ebe8

• Merge pull request #248 from ssjunnebo/add_changelog

  Show description for da7933d
  ssjunnebo

  authored
  da7933d

  Copy full SHA for da7933d

Commits on Dec 21, 2018

• Update TB panel to match new mykrobe panel

  martinghunt

  committed
  d6bee5d

  Copy full SHA for d6bee5d

• Version bump 2.13.2

  martinghunt

  committed
  dc7326c

  Copy full SHA for dc7326c

• Merge pull request #250 from martinghunt/update_tb_panel

  Show description for 680dc42
  martinghunt

  authored
  680dc42

  Copy full SHA for 680dc42

Commits on Jan 2, 2019

• Update tb panel with gyrA_D94A cipro resistance

  martinghunt

  committed
  dacdd71

  Copy full SHA for dacdd71

• Use latest panel files

  martinghunt

  committed
  941c08f

  Copy full SHA for 941c08f

• Version bump 2.13.3

  martinghunt

  committed
  1df5b3a

  Copy full SHA for 1df5b3a

• Merge pull request #251 from martinghunt/tb_D94A_fix

  Show description for 790f2bd
  martinghunt

  authored
  790f2bd

  Copy full SHA for 790f2bd

Commits on Jan 22, 2019

• Update README.md

  

  Mark Schultz

  authored
  3b78255

  Copy full SHA for 3b78255

Commits on Mar 12, 2019

• Added extra patterns

  kpepper

  committed
  565f802

  Copy full SHA for 565f802

• Updated version numbers

  kpepper

  committed
  e572be2

  Copy full SHA for e572be2

• Changed awk usage to gawk as awk does not support bitwise operations on OS X, leading to test failures

  kpepper

  committed
  da79fad

  Copy full SHA for da79fad

• Added ability to set CD-HIT memory limit on the command line - Issue #255

  kpepper

  committed
  70c82f5

  Copy full SHA for 70c82f5

Commits on Mar 13, 2019

• Changed some test asserts

  kpepper

  committed
  968659b

  Copy full SHA for 968659b

• Added some debug to track Docker test errors

  kpepper

  committed
  736955e

  Copy full SHA for 736955e

• Fixed some tests for the Docker build

  kpepper

  committed
  57430c7

  Copy full SHA for 57430c7

• Changed x's to upper case to see if this fixes the Docker build

  kpepper

  committed
  bb118b3

  Copy full SHA for bb118b3

• Revert "Changed x's to upper case to see if this fixes the Docker build"

  Show description for d0a8d71
  kpepper

  committed
  d0a8d71

  Copy full SHA for d0a8d71

Commits on Mar 14, 2019

• Changes to get Docker build working. Temporarily restricted pymummer version to 0.10.3 as later changes seem to break the ariba unit tests.

  kpepper

  committed
  f8b8b2a

  Copy full SHA for f8b8b2a

Commits on Mar 15, 2019

• Merge pull request #256 from kpepper/issue255_cd_hit_est_memory_feature

  Show description for f40cc15
  kpepper

  authored
  f40cc15

  Copy full SHA for f40cc15

• Rebuilt CHANGELOG

  kpepper

  committed
  64e0a2c

  Copy full SHA for 64e0a2c

• Merge pull request #257 from kpepper/update_changelog_for_v2.13.4

  Show description for 6a9d341
  kpepper

  authored
  6a9d341

  Copy full SHA for 6a9d341

Commits on Mar 21, 2019

• Minor code change to mitigate issue #245 (installation failure)

  kpepper

  committed
  2e53865

  Copy full SHA for 2e53865

• Merge pull request #258 from kpepper/fermilite_fix

  Show description for aa71cce
  kpepper

  authored
  aa71cce

  Copy full SHA for aa71cce

• Merge pull request #1 from sanger-pathogens/master

  Show description for d78445d
  kpepper

  authored
  d78445d

  Copy full SHA for d78445d

Commits on Mar 22, 2019

• Version number bump and updated CHANGELOG

  kpepper

  committed
  5b38230

  Copy full SHA for 5b38230

Commits on Mar 26, 2019

• Modified Spades invocation to force running with Python 3 (fix for Sanger environment)

  kpepper

  committed
  54860e2

  Copy full SHA for 54860e2

• Merge pull request #259 from kpepper/bump_version_to_2.13.5

  Show description for 0d708de
  kpepper

  authored
  0d708de

  Copy full SHA for 0d708de

• Updated to include latest PR

  kpepper

  committed
  e706fc6

  Copy full SHA for e706fc6

• Merge pull request #260 from kpepper/bump_version_to_2.13.5

  Show description for 16a0b19
  kpepper

  authored
  16a0b19

  Copy full SHA for 16a0b19

Commits on May 30, 2019

• Fixed merged of setup.py into ncbi branch on fork

  schultzm

  committed
  a14985c

  Copy full SHA for a14985c

• creating ncbi test on branch

  schultzm

  committed
  95ab2c7

  Copy full SHA for 95ab2c7

Commits on May 31, 2019

• Added unittest for ncbi

  schultzm

  committed
  d08f6c4

  Copy full SHA for d08f6c4

• Removed print statement under ncbi_getter

  schultzm

  committed
  9b59304

  Copy full SHA for 9b59304

Commits on Jun 4, 2019

• Removed call to sys.stderr, updated travis.yml py3.6

  schultzm

  committed
  8e75657

  Copy full SHA for 8e75657

• Added "ncbi" to line 65 of scripts/ariba

  schultzm

  committed
  1c4d422

  Copy full SHA for 1c4d422

• Merge pull request #269 from schultzm/ncbi

  Show description for 2203c7f
  kpepper

  authored
  2203c7f

  Copy full SHA for 2203c7f

Commits on Jun 5, 2019

• Changed SIGPIPE signal handling

  kpepper

  committed
  7c06df0

  Copy full SHA for 7c06df0

• Added extra info on Docker usage

  kpepper

  committed
  2c40be9

  Copy full SHA for 2c40be9

• Bumped Ubuntu and Ariba versions

  kpepper

  committed
  fcd06a2

  Copy full SHA for fcd06a2

• Changed required Python 3 and matplotlib versions

  kpepper

  committed
  d79500b

  Copy full SHA for d79500b

Commits on Jun 6, 2019

• Merge pull request #270 from sanger-pathogens/r2.14.0_update_branch

  Show description for c245d6c
  kpepper

  authored
  c245d6c

  Copy full SHA for c245d6c

• Updated CHANGELOG for release v2.14.0

  kpepper

  committed
  0ecc485

  Copy full SHA for 0ecc485

Commits on Jun 12, 2019

• Backed out MANIFEST.in change. Bumped release number to v2.14.1.

  kpepper

  committed
  2b088f4

  Copy full SHA for 2b088f4

Commits on Jun 13, 2019

• Fix for issue 263 - Ariba shutting down on receipt of SIGTSTP/SIGCONT

  kpepper

  committed
  2f673d7

  Copy full SHA for 2f673d7

• Merge pull request #271 from sanger-pathogens/v2.14.1_bug_fix_branch

  Show description for dae0008
  kpepper

  authored
  dae0008

  Copy full SHA for dae0008

Commits on Jun 14, 2019

• Added AUTHORS and LICENSE to the manifest so that they get included in PyPI and Bioconda distributions

  kpepper

  committed
  2c7166f

  Copy full SHA for 2c7166f

• Merge pull request #272 from sanger-pathogens/bioconda_license_fix

  Show description for 72ac778
  kpepper

  authored
  72ac778

  Copy full SHA for 72ac778

Commits on Jun 18, 2019

• Added Spades to docker file

  kpepper

  committed
  ec87112

  Copy full SHA for ec87112

• Bumped Ariba version number

  kpepper

  committed
  4bb8144

  Copy full SHA for 4bb8144

Commits on Jun 21, 2019

• Moved software version numbers into ARGs

  kpepper

  committed
  173ffbe

  Copy full SHA for 173ffbe

• Merge pull request #274 from sanger-pathogens/rt660940_add_spades_to_docker

  Show description for 105e426
  kpepper

  authored
  105e426

  Copy full SHA for 105e426

Commits on Jun 25, 2019

• Removed the specific Ariba release number and reconfigured the docker hub build

  kpepper

  committed
  53b14e5

  Copy full SHA for 53b14e5

• Merge pull request #276 from sanger-pathogens/dockerfile_ariba_version_upd

  Show description for 9cd5103
  kpepper

  authored
  9cd5103

  Copy full SHA for 9cd5103

Commits on Jun 26, 2019

• Remove extra matplotlib entry in install_requires

  Show description for fdf3ce2
  andersgs

  authored
  fdf3ce2

  Copy full SHA for fdf3ce2

Commits on Jun 27, 2019

• Merge pull request #277 from andersgs/fix_multiple_matplotlib_specs

  Show description for 71196cf
  kpepper

  authored
  71196cf

  Copy full SHA for 71196cf

Commits on Aug 9, 2019

• Fix for issue 278. And change the ariba git clone to a copy

  kpepper

  committed
  c69c9bb

  Copy full SHA for c69c9bb

• Bump Ariba version to 2.14.3

  kpepper

  committed
  af3b047

  Copy full SHA for af3b047

Commits on Aug 23, 2019

• Fix for issue #278 version 2

  kpepper

  committed
  868c995

  Copy full SHA for 868c995

Commits on Aug 30, 2019

• Merge pull request #279 from sanger-pathogens/cdhit_docker_fix_branch

  Show description for d1f1591
  kpepper

  authored
  d1f1591

  Copy full SHA for d1f1591

• Added default locale to fix an encoding error generated from getref for the card database when using docker

  kpepper

  committed
  601d4a8

  Copy full SHA for 601d4a8

• Merge pull request #280 from sanger-pathogens/cdhit_docker_fix_branch

  Show description for 3c95c7d
  kpepper

  authored
  3c95c7d

  Copy full SHA for 3c95c7d

Commits on Sep 24, 2019

• Fixed GitHub issue #281 - ARG-ANNOT Fails to Download. _get_from_argannot method has been updated accordingly

  kpepper

  committed
  2124ca6

  Copy full SHA for 2124ca6

• Merge pull request #282 from sanger-pathogens/argannot_issue281

  Show description for 4b7f8f2
  kpepper

  authored
  4b7f8f2

  Copy full SHA for 4b7f8f2

Commits on Nov 5, 2019

• Added unmaintained tag

  kpepper

  committed
  7de26b1

  Copy full SHA for 7de26b1

• Added unmaintained tag

  kpepper

  committed
  0fad90a

  Copy full SHA for 0fad90a

Commits on Nov 6, 2019

• Merge pull request #286 from sanger-pathogens/unmaintain_ariba

  Show description for 1075194
  kpepper

  authored
  1075194

  Copy full SHA for 1075194