Comments (5)
from fieldbioinformatics.
Hi @M-Artemisia. Thanks for getting in touch - and for offering to package this project!
There shouldn't be any Python2 in the source code for the current and future releases of fieldbioinformatics. We've kept a few pieces of Python2 under artic/deprecated
for posterity's sake but this isn't used in the current application. Is this a problem for packaging? We can look at removing it if needs be.
from fieldbioinformatics.
Thanks for your reply.
We are packaging the latest stable release V1.0.0, which is not in python3. As the next stable version (V1.1.0) would be in python3, I hope the v1.1.0-rc be released soon, so we could package it properly.
Also, there is not any problem about the artic/deprecated
directory in the next release. As all the python2 codes are gathered in a dedicated directory, it could be handled easily in packaging.
Hope to see the next stable relese soon,
best regards,
from fieldbioinformatics.
Hi @M-Artemisia
There is now a new release: https://github.com/artic-network/fieldbioinformatics/releases/tag/1.1.1
I hope this clears up the Python2/3 issues. Thank you again for packaging this for Debian!
from fieldbioinformatics.
Okay - I think we can close this now. Please re-open if you need anything else.
from fieldbioinformatics.
Related Issues (20)
- artic pipeline not installing properly: ModuleNotFoundError: No module named 'importlib.metadata' HOT 1
- Longshot `thread 'main' panicked at 'assertion failed: p <= 0.0'` error: possible to update longshot? HOT 3
- vcf_filter.py filtering parameters and align_trim.py for alternative primer scheme
- Error with medaka consensus HOT 1
- Unable to install artic on mac
- artic_vcf_merge Fails HOT 2
- What is the default mindepth ? HOT 4
- pipeline has stopped working...! HOT 5
- Conda recipe for 1.2.3 not working HOT 8
- no version information available (required by samtools) HOT 5
- Overlapping variants in fail.vcf and pass.vcf cause preconsensus to be masked and thus bcftools complains when applying the "pass" variant HOT 2
- Artic v5 mismatched primer names in bedfile causes "dropped" amplicons HOT 1
- Update medaka version HOT 2
- KeyError: 'SupportFraction' when running margin_cons.py
- Clarify what's meant by 'Suppress variant'
- Conda environment set up HOT 3
- Custom bed file with "primer gaps" causes workflow to crash at artic-tools vcf_checker step HOT 1
- Error: bcftools consensus fail with overlapping variants HOT 5
- htslib =1.17 dependency PLEASE UPDATE HOT 1
- PyVCF assigns a QUAL value of '.' instead of zero
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from fieldbioinformatics.