Closed Jiulong-Zhao closed 2 years ago
Hi Jiulong
Thank you for your interest in the method. I did some experimentation and experienced the same conflicts in the conda installation as you present here. Seems like the required scikit version is not compatible with Python v. 3.8.
Try to give this one a go, python 3.6 should not result in the same conflicts with scikit-learn and worked stable before.
conda create -n phamb python=3.6 cython scikit-learn==0.21.3 snakemake pygraphviz
Let me know if this works out.
Best, Joachim
And I check now with python=3.7
on Windows10, it does also seem to work:
conda create -c defaults -c conda-forge -c bioconda -n phamb snakemake pygraphviz python=3.7 cython scikit-learn=0.21.3
I added explicitly the list of anaconda channels in search order: -c defaults -c conda-forge -c bioconda
@joacjo @enryH Thanks for your kindly help!
Yeah, the installation of python=3.6 can work!
conda create -n phamb python=3.6 cython scikit-learn==0.21.3 snakemake pygraphviz
It can work, while "python=3.7" can not work in my CentOS 7.6 system.
Thanks again!
By the way, to my understanding, is this phamb workflow used to identify viral MAGs after binning by Vamb to obtain miscellaneous MAGs?
As python 3.6 is out of live, I guess it will be good to see if this can be updated..
@joacjo @enryH Thanks for your kindly help! Yeah, the installation of python=3.6 can work!
conda create -n phamb python=3.6 cython scikit-learn==0.21.3 snakemake pygraphviz
It can work, while "python=3.7" can not work in my CentOS 7.6 system.Thanks again!
By the way, to my understanding, is this phamb workflow used to identify viral MAGs after binning by Vamb to obtain miscellaneous MAGs?
Great it worked for you Jiulong! I will update the dependency for python 3.6, for now. As Henry points out, python 3.6 is getting outdated, so we will have to prepare the method for a more recent version of Python.
To your question, Yes phamb workflow requires Vamb clusters.tsv
and is optimised for that binner.
So you will need to run Vamb on a metagenomic dataset in order to employ this method.
Wish you all the best with your research!
Hi developer,
A very exciting work to develop this software to bin the phage genomes! Unfortunately, I meet some problems in starting to install the software. It seems like the Prerequisites you provided are conflicting and can not be installed simultaneously.
The errors log is as follows:
I also tried to install these packages one at a time and I also failed.
So, maybe the versions of these packages you provided are wrong?
Hope you can help me solve this issue!
Thank you so much!
Looking forward to your reply!
Jiulong