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sanger-pathogens / circlator

A tool to circularize genome assemblies
http://sanger-pathogens.github.io/circlator/
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canu version #152

Open aistBMRG opened 5 years ago

aistBMRG commented 5 years ago

Hi,

I assembled a genome using Canu v1.8 and wanted apply circlator v1.5.5.

Now, as a dependency, circlator can install Canu v1.4 -- can you clarify whether the versions should match?

Also, I found that when using Canu v1.8, seems that circlator fails to find the version due to a regrex issue, as has been pointed out and fix I thought ...

Can you clarify which is the better solution, install Canu 1.4 and use that although my assembly was with Canu 1.8, or fix the regrex issue.

Thanks.

Dieter

xpli2020 commented 3 years ago

Ssame issue here using canu 2.1.1, can not find canu version. There seems a thread indicating the authors had solved this issue in 2017. So I edited the code in the external_progs.py as below for matching canu version:

'canu':('-version', re.compile(r'canu ([\d+\.\d+[\.\d]*)')),

It passed the test run when running circlator test test_out

tnn111 commented 3 years ago

To solve this issue, simply install canu 2.1.1 using their installation instructions; i.e., do not use conda for it.

The one I ran into comes after that :-)

On Feb 28, 2021, at 07:08, xpli2020 notifications@github.com wrote:

Ssame issue here using canu 2.1.1, can not find canu version. There seems a thread indicating the authors had solved this issue in 2017.

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