new biopython version incompatible with HiCExplorer

[bgruening]

Welcome to the HiCExplorer GitHub repository! Before opening the issue please check
that the following requirements are met :

• Search whether this issue (or a similar issue) has been solved before using the search tab above. Link the previous issue if appropriate below.

• Paste your HiCExplorer version (hicInfo --version) and your python version (python --version) below.

• Have you checked our documentation on hicexplorer.readthedocs.io?

• Do you use conda to install HiCExplorer?

• Do you use the latest HiCExplorer release? If not, please install it via a conda environment:
  conda create --name hicexplorer hicexplorer=3.6 python=3.8 -c bioconda -c conda-forge
  and activate the environment: conda activate hicexplorer. Retry your command. You can exit a conda environment via conda deactivate. To learn more about conda and environments, please consider the following documentation.

The following is not supported anymore with the latest Biopthon release.

from Bio.Alphabet import generic_dna

And will results in a Traceback like:

Traceback (most recent call last):
  File "/home/bag/miniconda3/envs/mulled-v1-09ea340851a0a0d219d489590b2fe9df151628584a390fbd5b5e08cdd905038f/bin/hicBuildMatrix", line 4, in <module>
    from hicexplorer.hicBuildMatrix import main
  File "/home/bag/miniconda3/envs/mulled-v1-09ea340851a0a0d219d489590b2fe9df151628584a390fbd5b5e08cdd905038f/lib/python3.8/site-packages/hicexplorer/hicBuildMatrix.py", line 24, in <module>
    from Bio.Alphabet import generic_dna
  File "/home/bag/.local/lib/python3.8/site-packages/Bio/Alphabet/__init__.py", line 20, in <module>
    raise ImportError(
ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the ``molecule_type`` as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.

(mulled-v1-09ea340851a0a0d219d489590b2fe9df151628584a390fbd5b5e08cdd905038f) bag@bag:~/miniconda3/envs/[email protected]/lib$ hicexplorer --version
hicexplorer 3.6
(mulled-v1-09ea340851a0a0d219d489590b2fe9df151628584a390fbd5b5e08cdd905038f) bag@bag:~/miniconda3/envs/[email protected]/lib$ python --version
Python 3.8.5

[joachimwolff]

For this reason the biopython version is restricted to be smaller 1.77: https://github.com/deeptools/HiCExplorer/blob/master/requirements.txt#L8

https://github.com/bioconda/bioconda-recipes/blob/master/recipes/hicexplorer/meta.yaml#L28

However, even if we want to fix it, we need to wait for cooler to update to the new version: https://github.com/bioconda/bioconda-recipes/blob/master/recipes/cooler/meta.yaml#L24

[bgruening]

This is still true and refers to the code. I think it makes sense to leave it open until the code supports newer versions of biopython. Or did you fixed that in dev?

[NessieCanCode]

Hello Maintainers of HiCExplorer

using the following provided command for new setup/installs
conda create --name hicexplorer hicexplorer=3.6 python=3.8 -c bioconda -c conda-forge

Returns package python conflicts for:
hicexplorer=3.6 -> python[version='>=3.6']
python=3.8
hicexplorer=3.6 -> biopython[version='<1.77'] -> python[version='2.7.|3.5.|3.6.|3.4.|>=3.6,<3.7.0a0|>=2.7,<2.8.0a0|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0|<3.7|>=3.9,<3.10.0a0|>=3|<3.0.0|>=2.7|2.7|>=3.5']

This github issue seems to be related but not explicitly mentions new setups/installs

can you please advise on a possible workaround for this maybe a version of hicexplorer that still works for new installs,

[joachimwolff]

Hm, that worked today for me... Maybe some dependency was updated and causes now a conflict. Can you try the same command but add ˋcooler=0.8.9ˋ? As far as I know they had version 0.9 in the pipeline and that is the package which had biopython fixed to 1.77 so far.

[NessieCanCode]

using "conda create --name hicexplorer hicexplorer=3.6 cooler=0.8.9 python=3.8 -c bioconda -c conda-forge" increases the number of conflicts, but now I believe this might be related to the conda version, I did a fresh install of anaconda3-2020.11 on a test vm and installed without issue, the cluster I'm having an issue on is running a older version 4.8.4

Package python conflicts for:
cooler=0.8.9 -> python
hicexplorer=3.6 -> biopython[version='<1.77'] -> python[version='2.7.|3.5.|3.6.|3.4.|>=3.6,<3.7.0a0|>=2.7,<2.8.0a0|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0|<3.7|>=3.9,<3.10.0a0|>=3|<3.0.0|>=2.7|2.7|>=3.5']
hicexplorer=3.6 -> python[version='>=3.6']
cooler=0.8.9 -> asciitree -> python[version='2.7.|3.5.|3.6.|3.4.|>=3.6,<3.7.0a0|>=2.7,<2.8.0a0|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0|>=3.9,<3.10.0a0|>=3.7|>=3.6|>=3.5']
python=3.8

Package setuptools conflicts for:
hicexplorer=3.6 -> hyperopt[version='>=0.2.4'] -> setuptools
python=3.8 -> pip -> setuptools

Package ca-certificates conflicts for:
cooler=0.8.9 -> python -> ca-certificates
python=3.8 -> openssl[version='>=1.1.1j,<1.1.2a'] -> ca-certificates

Package cooler conflicts for:
hicexplorer=3.6 -> cooler[version='>=0.8.10']
cooler=0.8.9
hicexplorer=3.6 -> hic2cool[version='>=0.8.3'] -> cooler[version='>=0.8.5']

[joachimwolff]

I think the issue needs be solved by updating your conda installation, maybe you can report this as a bug to conda itself.
The only idea I have to get it installed is to try a older python version, maybe 3.6 or 3.7 work with the outdated conda version?

[joachimwolff]

Biopython version fixed by Lucille PR #718.