Update - Patches for third party links used by Ariba #24010

rpetit3 · 2020-08-19T21:49:58Z

This PR includes two patches for Ariba related to changes in API endpoints.

pubmlst_getter.patch fixes broken PubMLST downloads due to a change in API endpoint.

Original Issue: sanger-pathogens/ariba#304

Submitted Ariba PR: sanger-pathogens/ariba#305

ref_genes_getter.patch fixes a change in CARD links that causes RGI to be downloading instead of CARD

Original Issue: sanger-pathogens/ariba#301

Submitted Ariba PR: sanger-pathogens/ariba#303

This my first time submitting a PR with patches so any advice would be appreaciated. I generated the patches through GitHub by appending .patch to the PR link.

https://github.com/sanger-pathogens/ariba/pull/303.patch

https://github.com/sanger-pathogens/ariba/pull/305.patch

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rpetit3 · 2020-08-19T22:11:40Z

@bioconda-bot please fetch artifacts

BiocondaBot · 2020-08-19T22:12:17Z

Package(s) built on CircleCI are ready for inspection:

Arch	Package	Repodata
linux-64	ariba-2.14.5-py36hf0b53f7_2.tar.bz2	repodata.json
linux-64	ariba-2.14.5-py37hfa133b6_2.tar.bz2	repodata.json
osx-64	ariba-2.14.5-py36h043d725_2.tar.bz2	repodata.json
osx-64	ariba-2.14.5-py37hbeab489_2.tar.bz2	repodata.json

You may also use conda to install these:

For packages on linux-64:

conda install -c https://120647-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>

For packages on osx-64:

conda install -c https://120648-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>

Docker image(s) built:

Package	Tag	Install with `docker`
ariba	2.14.5--py36hf0b53f7_2	show `curl "https://120647-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/ariba%3A2.14.5--py36hf0b53f7_2.tar.gz" \| gzip -dc \| docker load`
ariba	2.14.5--py37hfa133b6_2	show `curl "https://120647-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/ariba%3A2.14.5--py37hfa133b6_2.tar.gz" \| gzip -dc \| docker load`

rpetit3 · 2020-08-19T22:13:22Z

I'm going to test locally, to verify patches worked

rpetit3 · 2020-08-19T23:10:12Z

conda create -n ariba2 -c https://120647-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages -c conda-forge -c bioconda 
conda activate

# Get ariba version
ariba version
Traceback (most recent call last):
  File "/local/home/rpetit/miniconda3/envs/ariba2/bin/ariba", line 312, in <module>
    args.func(args)
  File "/local/home/rpetit/miniconda3/envs/ariba2/lib/python3.6/site-packages/ariba/tasks/version.py", line 5, in run
    extern_progs, report_lines = versions.get_all_versions(raise_error=False)
  File "/local/home/rpetit/miniconda3/envs/ariba2/lib/python3.6/site-packages/ariba/versions.py", line 21, in get_all_versions
    extern_progs = external_progs.ExternalProgs(fail_on_error=False, using_spades=using_spades)
  File "/local/home/rpetit/miniconda3/envs/ariba2/lib/python3.6/site-packages/ariba/external_progs.py", line 89, in __init__
    if prog in min_versions and LooseVersion(version) < LooseVersion(min_versions[prog]):
  File "/local/home/rpetit/miniconda3/envs/ariba2/lib/python3.6/distutils/version.py", line 52, in __lt__
    c = self._cmp(other)
  File "/local/home/rpetit/miniconda3/envs/ariba2/lib/python3.6/distutils/version.py", line 335, in _cmp
    if self.version == other.version:
AttributeError: 'LooseVersion' object has no attribute 'version'

# Current Bioconda version of Bowtie2 doesn't output version correctly
conda install -y -c conda-forge -c bioconda bowtie2=2.3.5

# Test version again
ariba version
WARNING: I tried to get the version of spades with: "/local/home/rpetit/miniconda3/envs/ariba2/bin/spades.py --version" and the output didn't match this regular expression: "SPAdes\s+v([0-9\.]+)"
ARIBA version: 2.14.5

External dependencies:
bowtie2 2.3.5.1 /local/home/rpetit/miniconda3/envs/ariba2/bin/bowtie2
cdhit   4.8.1   /local/home/rpetit/miniconda3/envs/ariba2/bin/cd-hit-est
nucmer  3.1     /local/home/rpetit/miniconda3/envs/ariba2/bin/nucmer
spades  ERROR   /local/home/rpetit/miniconda3/envs/ariba2/bin/spades.py

External dependencies OK: True

Python version:
3.6.11 | packaged by conda-forge | (default, Aug  5 2020, 20:09:42)
[GCC 7.5.0]

Python packages:
ariba   2.14.5  /local/home/rpetit/miniconda3/envs/ariba2/lib/python3.6/site-packages/ariba/__init__.py
bs4     4.9.1   /local/home/rpetit/miniconda3/envs/ariba2/lib/python3.6/site-packages/bs4/__init__.py
dendropy        4.4.0   /local/home/rpetit/miniconda3/envs/ariba2/lib/python3.6/site-packages/dendropy/__init__.py
pyfastaq        3.17.0  /local/home/rpetit/miniconda3/envs/ariba2/lib/python3.6/site-packages/pyfastaq/__init__.py
pymummer        0.10.3  /local/home/rpetit/miniconda3/envs/ariba2/lib/python3.6/site-packages/pymummer/__init__.py
pysam   0.16.0.1        /local/home/rpetit/miniconda3/envs/ariba2/lib/python3.6/site-packages/pysam/__init__.py

Python packages OK: True

Everything looks OK: True

# Test PubMLST
ariba pubmlstget "Staphylococcus aureus" test_pubmlst
WARNING: I tried to get the version of spades with: "/local/home/rpetit/miniconda3/envs/ariba2/bin/spades.py --version" and the output didn't match this regular expression: "SPAdes\s+v([0-9\.]+)"
WARNING: Median sequence length is 456 but arcC.548 has length 522 which is too long or short. Removing.
WARNING: Median sequence length is 456 but arcC.567 has length 516 which is too long or short. Removing.
ariba db directory prepared. You can use it like this:
ariba run test_pubmlst/ref_db reads_1.fq reads_2.fq output_directory

ls test_pubmlst/pubmlst_download/
arcC.tfa  aroE.tfa  glpF.tfa  gmk.tfa  profile.txt  pta.tfa  tpi.tfa  yqiL.tfa

# Test Card
ariba getref card card
Getting available CARD versions
Downloading "https://card.mcmaster.ca/download" and saving as "download.html" ... done
Found versions:
1.0.0   https://card.mcmaster.ca/download/0/broadstreet-v1.0.0.tar.bz2
1.0.1   https://card.mcmaster.ca/download/0/broadstreet-v1.0.1.tar.bz2
1.0.2   https://card.mcmaster.ca/download/0/broadstreet-v1.0.2.tar.bz2
1.0.3   https://card.mcmaster.ca/download/0/broadstreet-v1.0.3.tar.bz2
1.0.4   https://card.mcmaster.ca/download/0/broadstreet-v1.0.4.tar.bz2
1.0.5   https://card.mcmaster.ca/download/0/broadstreet-v1.0.5.tar.bz2
1.0.6   https://card.mcmaster.ca/download/0/broadstreet-v1.0.6.tar.bz2
1.0.7   https://card.mcmaster.ca/download/0/broadstreet-v1.0.7.tar.bz2
1.0.8   https://card.mcmaster.ca/download/0/broadstreet-v1.0.8.tar.bz2
1.0.9   https://card.mcmaster.ca/download/0/broadstreet-v1.0.9.tar.bz2
1.1.0   https://card.mcmaster.ca/download/0/broadstreet-v1.1.0.tar.bz2
1.1.1   https://card.mcmaster.ca/download/0/broadstreet-v1.1.1.tar.bz2
1.1.2   https://card.mcmaster.ca/download/0/broadstreet-v1.1.2.tar.bz2
1.1.3   https://card.mcmaster.ca/download/0/broadstreet-v1.1.3.tar.bz2
1.1.4   https://card.mcmaster.ca/download/0/broadstreet-v1.1.4.tar.bz2
1.1.5   https://card.mcmaster.ca/download/0/broadstreet-v1.1.5.tar.bz2
1.1.6   https://card.mcmaster.ca/download/0/broadstreet-v1.1.6.tar.bz2
1.1.7   https://card.mcmaster.ca/download/0/broadstreet-v1.1.7.tar.bz2
1.1.8   https://card.mcmaster.ca/download/0/broadstreet-v1.1.8.tar.bz2
1.1.9   https://card.mcmaster.ca/download/0/broadstreet-v1.1.9.tar.bz2
1.2.0   https://card.mcmaster.ca/download/0/broadstreet-v1.2.0.tar.bz2
1.2.1   https://card.mcmaster.ca/download/0/broadstreet-v1.2.1.tar.bz2
2.0.0   https://card.mcmaster.ca/download/0/broadstreet-v2.0.0.tar.gz
2.0.1   https://card.mcmaster.ca/download/0/broadstreet-v2.0.1.tar.gz
2.0.2   https://card.mcmaster.ca/download/0/broadstreet-v2.0.2.tar.gz
2.0.3   https://card.mcmaster.ca/download/0/broadstreet-v2.0.3.tar.gz
3.0.0   https://card.mcmaster.ca/download/0/broadstreet-v3.0.0.tar.gz
3.0.1   https://card.mcmaster.ca/download/0/broadstreet-v3.0.1.tar.gz
3.0.2   https://card.mcmaster.ca/download/0/broadstreet-v3.0.2.tar.gz
3.0.3   https://card.mcmaster.ca/download/0/broadstreet-v3.0.3.tar.gz
3.0.4   https://card.mcmaster.ca/download/0/broadstreet-v3.0.4.tar.gz
3.0.5   https://card.mcmaster.ca/download/0/broadstreet-v3.0.5.tar.gz
3.0.6   https://card.mcmaster.ca/download/0/broadstreet-v3.0.6.tar.gz
3.0.7   https://card.mcmaster.ca/download/0/broadstreet-v3.0.7.tar.gz
3.0.8   https://card.mcmaster.ca/download/0/broadstreet-v3.0.8.tar.bz2
3.0.9   https://card.mcmaster.ca/download/0/broadstreet-v3.0.9.tar.bz2
3.1.0   https://card.mcmaster.ca/download/0/broadstreet-v3.1.0.tar.bz2
Getting version 3.1.0
Working in temporary directory /local/home/rpetit/temp_blast/card.download
Downloading data from card: https://card.mcmaster.ca/download/0/broadstreet-v3.1.0.tar.bz2
syscall: wget -O card.tar.bz2 https://card.mcmaster.ca/download/0/broadstreet-v3.1.0.tar.bz2
...finished downloading
Extracted json data file ./card.json. Reading its contents...
Found 3022 records in the json file. Analysing...
Extracted data and written ARIBA input files

Finished. Final files are:
        /local/home/rpetit/temp_blast/card.fa
        /local/home/rpetit/temp_blast/card.tsv

You can use them with ARIBA like this:
ariba prepareref -f /local/home/rpetit/temp_blast/card.fa -m /local/home/rpetit/temp_blast/card.tsv output_directory

If you use this downloaded data, please cite:
"The Comprehensive Antibiotic Resistance Database", McArthur et al 2013, PMID: 23650175
and in your methods say that version 3.1.0 of the database was used

Looks like everything is working correctly. I'm going to pin the version of Bowtie2 to be <2.4 (See for more info: #22836)

Test version, since there are open Issues related to bowtie2 version info and it affects ariba

rpetit3 · 2020-08-20T00:16:40Z

@bioconda-bot please fetch artifacts

rpetit3 · 2020-08-20T00:16:50Z

@bioconda-bot please label

BiocondaBot · 2020-08-20T00:17:17Z

Package(s) built on CircleCI are ready for inspection:

Arch	Package	Repodata
linux-64	ariba-2.14.5-py36hf0b53f7_2.tar.bz2	repodata.json
linux-64	ariba-2.14.5-py37hfa133b6_2.tar.bz2	repodata.json
osx-64	ariba-2.14.5-py36h043d725_2.tar.bz2	repodata.json
osx-64	ariba-2.14.5-py37hbeab489_2.tar.bz2	repodata.json

You may also use conda to install these:

For packages on linux-64:

conda install -c https://120660-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>

For packages on osx-64:

conda install -c https://120661-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>

Docker image(s) built:

Package	Tag	Install with `docker`
ariba	2.14.5--py36hf0b53f7_2	show `curl "https://120660-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/ariba%3A2.14.5--py36hf0b53f7_2.tar.gz" \| gzip -dc \| docker load`
ariba	2.14.5--py37hfa133b6_2	show `curl "https://120660-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/ariba%3A2.14.5--py37hfa133b6_2.tar.gz" \| gzip -dc \| docker load`

rpetit3 · 2020-08-20T00:19:19Z

@bioconda-bot please add label

rpetit3 · 2020-08-20T00:23:32Z

Retested, good to go

(base) rpetit@staphopia:~$ conda create -y -n ariba-patched -c https://120660-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages -c conda-forge -c bioconda ariba
(base) rpetit@staphopia:~$ conda activate ariba-patched
(ariba-patched) rpetit@staphopia:~$ ariba version
WARNING: I tried to get the version of spades with: "/local/home/rpetit/miniconda3/envs/ariba-patched/bin/spades.py --version" and the output didn't match this regular expression: "SPAdes\s+v([0-9\.]+)"
ARIBA version: 2.14.5

External dependencies:
bowtie2 2.3.5.1 /local/home/rpetit/miniconda3/envs/ariba-patched/bin/bowtie2
cdhit   4.8.1   /local/home/rpetit/miniconda3/envs/ariba-patched/bin/cd-hit-est
nucmer  3.1     /local/home/rpetit/miniconda3/envs/ariba-patched/bin/nucmer
spades  ERROR   /local/home/rpetit/miniconda3/envs/ariba-patched/bin/spades.py

External dependencies OK: True

Python version:
3.6.11 | packaged by conda-forge | (default, Aug  5 2020, 20:09:42)
[GCC 7.5.0]

Python packages:
ariba   2.14.5  /local/home/rpetit/miniconda3/envs/ariba-patched/lib/python3.6/site-packages/ariba/__init__.py
bs4     4.9.1   /local/home/rpetit/miniconda3/envs/ariba-patched/lib/python3.6/site-packages/bs4/__init__.py
dendropy        4.4.0   /local/home/rpetit/miniconda3/envs/ariba-patched/lib/python3.6/site-packages/dendropy/__init__.py
pyfastaq        3.17.0  /local/home/rpetit/miniconda3/envs/ariba-patched/lib/python3.6/site-packages/pyfastaq/__init__.py
pymummer        0.10.3  /local/home/rpetit/miniconda3/envs/ariba-patched/lib/python3.6/site-packages/pymummer/__init__.py
pysam   0.16.0.1        /local/home/rpetit/miniconda3/envs/ariba-patched/lib/python3.6/site-packages/pysam/__init__.py

Python packages OK: True

Everything looks OK: True
(ariba-patched) rpetit@staphopia:~$ cd temp_blast/
(ariba-patched) rpetit@staphopia:~/temp_blast$ ariba pubmlstget "Staphylococcus aureus" test_pubmlst2
WARNING: I tried to get the version of spades with: "/local/home/rpetit/miniconda3/envs/ariba-patched/bin/spades.py --version" and the output didn't match this regular expression: "SPAdes\s+v([0-9\.]+)"
WARNING: Median sequence length is 456 but arcC.548 has length 522 which is too long or short. Removing.
WARNING: Median sequence length is 456 but arcC.567 has length 516 which is too long or short. Removing.
ariba db directory prepared. You can use it like this:
ariba run test_pubmlst2/ref_db reads_1.fq reads_2.fq output_directory
(ariba-patched) rpetit@staphopia:~/temp_blast$ ariba getref card card
Getting available CARD versions
Downloading "https://card.mcmaster.ca/download" and saving as "download.html" ... done
Found versions:
1.0.0   https://card.mcmaster.ca/download/0/broadstreet-v1.0.0.tar.bz2
1.0.1   https://card.mcmaster.ca/download/0/broadstreet-v1.0.1.tar.bz2
1.0.2   https://card.mcmaster.ca/download/0/broadstreet-v1.0.2.tar.bz2
1.0.3   https://card.mcmaster.ca/download/0/broadstreet-v1.0.3.tar.bz2
1.0.4   https://card.mcmaster.ca/download/0/broadstreet-v1.0.4.tar.bz2
1.0.5   https://card.mcmaster.ca/download/0/broadstreet-v1.0.5.tar.bz2
1.0.6   https://card.mcmaster.ca/download/0/broadstreet-v1.0.6.tar.bz2
1.0.7   https://card.mcmaster.ca/download/0/broadstreet-v1.0.7.tar.bz2
1.0.8   https://card.mcmaster.ca/download/0/broadstreet-v1.0.8.tar.bz2
1.0.9   https://card.mcmaster.ca/download/0/broadstreet-v1.0.9.tar.bz2
1.1.0   https://card.mcmaster.ca/download/0/broadstreet-v1.1.0.tar.bz2
1.1.1   https://card.mcmaster.ca/download/0/broadstreet-v1.1.1.tar.bz2
1.1.2   https://card.mcmaster.ca/download/0/broadstreet-v1.1.2.tar.bz2
1.1.3   https://card.mcmaster.ca/download/0/broadstreet-v1.1.3.tar.bz2
1.1.4   https://card.mcmaster.ca/download/0/broadstreet-v1.1.4.tar.bz2
1.1.5   https://card.mcmaster.ca/download/0/broadstreet-v1.1.5.tar.bz2
1.1.6   https://card.mcmaster.ca/download/0/broadstreet-v1.1.6.tar.bz2
1.1.7   https://card.mcmaster.ca/download/0/broadstreet-v1.1.7.tar.bz2
1.1.8   https://card.mcmaster.ca/download/0/broadstreet-v1.1.8.tar.bz2
1.1.9   https://card.mcmaster.ca/download/0/broadstreet-v1.1.9.tar.bz2
1.2.0   https://card.mcmaster.ca/download/0/broadstreet-v1.2.0.tar.bz2
1.2.1   https://card.mcmaster.ca/download/0/broadstreet-v1.2.1.tar.bz2
2.0.0   https://card.mcmaster.ca/download/0/broadstreet-v2.0.0.tar.gz
2.0.1   https://card.mcmaster.ca/download/0/broadstreet-v2.0.1.tar.gz
2.0.2   https://card.mcmaster.ca/download/0/broadstreet-v2.0.2.tar.gz
2.0.3   https://card.mcmaster.ca/download/0/broadstreet-v2.0.3.tar.gz
3.0.0   https://card.mcmaster.ca/download/0/broadstreet-v3.0.0.tar.gz
3.0.1   https://card.mcmaster.ca/download/0/broadstreet-v3.0.1.tar.gz
3.0.2   https://card.mcmaster.ca/download/0/broadstreet-v3.0.2.tar.gz
3.0.3   https://card.mcmaster.ca/download/0/broadstreet-v3.0.3.tar.gz
3.0.4   https://card.mcmaster.ca/download/0/broadstreet-v3.0.4.tar.gz
3.0.5   https://card.mcmaster.ca/download/0/broadstreet-v3.0.5.tar.gz
3.0.6   https://card.mcmaster.ca/download/0/broadstreet-v3.0.6.tar.gz
3.0.7   https://card.mcmaster.ca/download/0/broadstreet-v3.0.7.tar.gz
3.0.8   https://card.mcmaster.ca/download/0/broadstreet-v3.0.8.tar.bz2
3.0.9   https://card.mcmaster.ca/download/0/broadstreet-v3.0.9.tar.bz2
3.1.0   https://card.mcmaster.ca/download/0/broadstreet-v3.1.0.tar.bz2
Getting version 3.1.0
Working in temporary directory /local/home/rpetit/temp_blast/card.download
Downloading data from card: https://card.mcmaster.ca/download/0/broadstreet-v3.1.0.tar.bz2
syscall: wget -O card.tar.bz2 https://card.mcmaster.ca/download/0/broadstreet-v3.1.0.tar.bz2
...finished downloading
Extracted json data file ./card.json. Reading its contents...
Found 3022 records in the json file. Analysing...
Extracted data and written ARIBA input files

Finished. Final files are:
        /local/home/rpetit/temp_blast/card.fa
        /local/home/rpetit/temp_blast/card.tsv

You can use them with ARIBA like this:
ariba prepareref -f /local/home/rpetit/temp_blast/card.fa -m /local/home/rpetit/temp_blast/card.tsv output_directory

If you use this downloaded data, please cite:
"The Comprehensive Antibiotic Resistance Database", McArthur et al 2013, PMID: 23650175
and in your methods say that version 3.1.0 of the database was used

simonbray · 2020-08-20T08:41:01Z

@bioconda-bot please merge

Looks good @rpetit3

BiocondaBot · 2020-08-20T08:41:37Z

I will attempt to upload artifacts and merge this PR. This may take some time, please have patience.

rpetit3 added 3 commits August 19, 2020 17:32

Create ref_genes_getter.patch

f4498af

Create pubmlst_getter.patch

1d94900

Update meta.yaml

9eb6f0c

This was referenced Aug 19, 2020

datasets card download issue bactopia/bactopia#113

Closed

[bug] Bactopia Datasets - Ariba fails to download PubMLST schemas bactopia/bactopia#118

Closed

rpetit3 added 3 commits August 19, 2020 19:12

Update meta.yaml

a3529d8

Update meta.yaml

142d138

Update meta.yaml

d499f60

Test version, since there are open Issues related to bowtie2 version info and it affects ariba

BiocondaBot added the please review & merge set to ask for merge label Aug 20, 2020

simonbray approved these changes Aug 20, 2020

View reviewed changes

BiocondaBot merged commit b65890c into master Aug 20, 2020

BiocondaBot deleted the rpetit3-ariba-patch-1 branch August 20, 2020 08:46

oliver-tarrant-tessella mentioned this pull request Sep 16, 2020

Set bowtie version to <2.4 ngs-mstb/ngs-mstb-conda#1

Closed

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Update - Patches for third party links used by Ariba #24010

Update - Patches for third party links used by Ariba #24010

rpetit3 commented Aug 19, 2020 •

edited

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rpetit3 commented Aug 19, 2020

BiocondaBot commented Aug 19, 2020

rpetit3 commented Aug 19, 2020

rpetit3 commented Aug 19, 2020

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Update - Patches for third party links used by Ariba #24010

Update - Patches for third party links used by Ariba #24010

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rpetit3 commented Aug 19, 2020 • edited Loading

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rpetit3 commented Aug 19, 2020 •

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