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sanger-pathogens / ariba

Antimicrobial Resistance Identification By Assembly
http://sanger-pathogens.github.io/ariba/
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fix SPAdes version capture #315

Closed rpetit3 closed 3 years ago

rpetit3 commented 3 years ago

This is related to https://github.com/sanger-pathogens/ariba/issues/314

At some point SPAdes changed their --version output, causing the warning message from ariba --version

spades.py --version
SPAdes genome assembler v3.15.2
ariba version
WARNING: I tried to get the version of spades with: "/home/robert_petit/miniconda3/envs/ariba/bin/spades.py --version" and the output didn't match this regular expression: "SPAdes\s+v([0-9\.]+)"
ARIBA version: 2.14.6

External dependencies:
bowtie2 2.2.5   /home/robert_petit/miniconda3/envs/ariba/bin/bowtie2
cdhit   4.8.1   /home/robert_petit/miniconda3/envs/ariba/bin/cd-hit-est
nucmer  3.1     /home/robert_petit/miniconda3/envs/ariba/bin/nucmer
spades  ERROR   /home/robert_petit/miniconda3/envs/ariba/bin/spades.py

External dependencies OK: True

Python version:
3.8.10 | packaged by conda-forge | (default, May 11 2021, 07:01:05)
[GCC 9.3.0]

Python packages:
ariba   2.14.6  /home/robert_petit/miniconda3/envs/ariba/lib/python3.8/site-packages/ariba/__init__.py
bs4     4.9.3   /home/robert_petit/miniconda3/envs/ariba/lib/python3.8/site-packages/bs4/__init__.py
dendropy        4.5.2   /home/robert_petit/miniconda3/envs/ariba/lib/python3.8/site-packages/dendropy/__init__.py
pyfastaq        3.17.0  /home/robert_petit/miniconda3/envs/ariba/lib/python3.8/site-packages/pyfastaq/__init__.py
pymummer        0.10.3  /home/robert_petit/miniconda3/envs/ariba/lib/python3.8/site-packages/pymummer/__init__.py
pysam   0.16.0.1        /home/robert_petit/miniconda3/envs/ariba/lib/python3.8/site-packages/pysam/__init__.py

Python packages OK: True

Everything looks OK: True

With fix to regex

ariba version
ARIBA version: 2.14.6

External dependencies:
bowtie2 2.2.5   /home/robert_petit/miniconda3/envs/ariba/bin/bowtie2
cdhit   4.8.1   /home/robert_petit/miniconda3/envs/ariba/bin/cd-hit-est
nucmer  3.1     /home/robert_petit/miniconda3/envs/ariba/bin/nucmer
spades  3.15.2  /home/robert_petit/miniconda3/envs/ariba/bin/spades.py

External dependencies OK: True

Python version:
3.8.10 | packaged by conda-forge | (default, May 11 2021, 07:01:05)
[GCC 9.3.0]

Python packages:
ariba   2.14.6  /home/robert_petit/miniconda3/envs/ariba/lib/python3.8/site-packages/ariba/__init__.py
bs4     4.9.3   /home/robert_petit/miniconda3/envs/ariba/lib/python3.8/site-packages/bs4/__init__.py
dendropy        4.5.2   /home/robert_petit/miniconda3/envs/ariba/lib/python3.8/site-packages/dendropy/__init__.py
pyfastaq        3.17.0  /home/robert_petit/miniconda3/envs/ariba/lib/python3.8/site-packages/pyfastaq/__init__.py
pymummer        0.10.3  /home/robert_petit/miniconda3/envs/ariba/lib/python3.8/site-packages/pymummer/__init__.py
pysam   0.16.0.1        /home/robert_petit/miniconda3/envs/ariba/lib/python3.8/site-packages/pysam/__init__.py

Python packages OK: True

Everything looks OK: True

With previous version of SPAdes

spades.py --version
SPAdes v3.13.0
ARIBA version: 2.14.6

External dependencies:
bowtie2 2.2.5   /home/robert_petit/miniconda3/envs/ariba/bin/bowtie2
cdhit   4.8.1   /home/robert_petit/miniconda3/envs/ariba/bin/cd-hit-est
nucmer  3.1     /home/robert_petit/miniconda3/envs/ariba/bin/nucmer
spades  3.13.0  /home/robert_petit/miniconda3/envs/ariba/bin/spades.py

External dependencies OK: True

Python version:
3.8.10 | packaged by conda-forge | (default, May 11 2021, 07:01:05)
[GCC 9.3.0]

Python packages:
ariba   2.14.6  /home/robert_petit/miniconda3/envs/ariba/lib/python3.8/site-packages/ariba/__init__.py
bs4     4.9.3   /home/robert_petit/miniconda3/envs/ariba/lib/python3.8/site-packages/bs4/__init__.py
dendropy        4.5.2   /home/robert_petit/miniconda3/envs/ariba/lib/python3.8/site-packages/dendropy/__init__.py
pyfastaq        3.17.0  /home/robert_petit/miniconda3/envs/ariba/lib/python3.8/site-packages/pyfastaq/__init__.py
pymummer        0.10.3  /home/robert_petit/miniconda3/envs/ariba/lib/python3.8/site-packages/pymummer/__init__.py
pysam   0.16.0.1        /home/robert_petit/miniconda3/envs/ariba/lib/python3.8/site-packages/pysam/__init__.py

Python packages OK: True

Everything looks OK: True
puethe commented 3 years ago

Thanks!