nucmer version isn't detected correctly

[lfaller]

Hi all,

I installed circlator from a github clone. Unfortunately, it can't detect the nucmer version correctly.

$ circlator progcheck
Circlator version: 1.5.2

External dependencies:
bwa     0.7.15  /home/lina/bin/bwa
canu    1.6     /home/lina/canu-1.6/Linux-amd64/bin/canu
Found nucmer but couldn't get version.
prodigal        2.6.3   /home/lina/bin/prodigal
samtools        1.3.1   /home/lina/bin/samtools
WARNING: SPAdes version 3.10.1 is being used. It will work, but better results are usually obtained from Circlator using SPAdes version 3.7.1. Although 3.7.1 is not the latest version, we recommend it for Circlator.
spades  3.10.1  /home/lina/SPAdes-3.10.1-Linux/bin/spades.py

Python version:
3.5.2 (default, Sep 14 2017, 22:51:06)
[GCC 5.4.0 20160609]

Python dependencies:
openpyxl        2.4.9   /home/lina/.local/lib/python3.5/site-packages/openpyxl/__init__.py
pyfastaq        3.15.0  /home/lina/.local/lib/python3.5/site-packages/pyfastaq/__init__.py
pymummer        0.10.3  /home/lina/.local/lib/python3.5/site-packages/pymummer/__init__.py
pysam   0.12.0.1        /home/lina/.local/lib/python3.5/site-packages/pysam/__init__.py

I do have nucmer installed:

nucmer --version
4.0.0beta1

Looking at the regular expression you used, I think it's not matching the version format:

'nucmer': ('--version', re.compile('^NUCmer \(NUCleotide MUMmer\) version ([0-9\.]+)')),

Do you support the newer versions of nucmer? Or should I install one of the older versions?

Thanks for any advice!

[spock]

Newer versions seem to be working fine, but I haven't properly tested against older versions, see #110 (comment)

[lfaller]

Thank you @spock -- I was able to modify the regular expression as you described and now circlator is running.

[RightCake1]

Hi all,

I installed circlator from a github clone. Unfortunately, it can't detect the nucmer version correctly.

$ circlator progcheck
Circlator version: 1.5.2

External dependencies:
bwa     0.7.15  /home/lina/bin/bwa
canu    1.6     /home/lina/canu-1.6/Linux-amd64/bin/canu
Found nucmer but couldn't get version.
prodigal        2.6.3   /home/lina/bin/prodigal
samtools        1.3.1   /home/lina/bin/samtools
WARNING: SPAdes version 3.10.1 is being used. It will work, but better results are usually obtained from Circlator using SPAdes version 3.7.1. Although 3.7.1 is not the latest version, we recommend it for Circlator.
spades  3.10.1  /home/lina/SPAdes-3.10.1-Linux/bin/spades.py

Python version:
3.5.2 (default, Sep 14 2017, 22:51:06)
[GCC 5.4.0 20160609]

Python dependencies:
openpyxl        2.4.9   /home/lina/.local/lib/python3.5/site-packages/openpyxl/__init__.py
pyfastaq        3.15.0  /home/lina/.local/lib/python3.5/site-packages/pyfastaq/__init__.py
pymummer        0.10.3  /home/lina/.local/lib/python3.5/site-packages/pymummer/__init__.py
pysam   0.12.0.1        /home/lina/.local/lib/python3.5/site-packages/pysam/__init__.py

I do have nucmer installed:

nucmer --version
4.0.0beta1

Looking at the regular expression you used, I think it's not matching the version format:

'nucmer': ('--version', re.compile('^NUCmer \(NUCleotide MUMmer\) version ([0-9\.]+)')),

Do you support the newer versions of nucmer? Or should I install one of the older versions?

Thanks for any advice!

Hi i'm new to ubuntu. Could you please tell me how i can update my nucmer to the latest version?