VIBRANT cannot setup in puthon 3.8?

[ZhengXiaoxuan11542]

Hi @KrisKieft,

thank you very much for creating such a brilliant instruction first! I have run VIBRANT successfully on my old server as well as cyverse with nice results before. However, I cannot install the latest VIBRANT on my new server when I want to start my new work. I noticed that the VIBRANT relies on the package Scikit-learn ==0.21.3, which is now updated to version 1.1 and requires Python 3.8 ( which is my version) or newer. Will VIBRANT update the dependencies in the nearly future? Or do I just have to rebuild older Versions of Python to solve this problem?

Kind regards, Xiaoxuan

[KrisKieft]

Hi,

The sklearn dependency will not be updated in the near future as that will require a full re-build of the machine learning model. Do you have conda installed? That can be a useful method to construct a virtual environment in which to install the older sklearn and Python versions.

Kris

[ZhengXiaoxuan11542]

Hi,

The sklearn dependency will not be updated in the near future as that will require a full re-build of the machine learning model. Do you have conda installed? That can be a useful method to construct a virtual environment in which to install the older sklearn and Python versions.

Kris

Hi Kris, So glad to have your reply. Construct an older python virtual environment is truly a good idea and now I have almost installed VIBRANT successfully in python 3.7. However, an error occurred when I tried to run the example data: VIBRANT error: could not identify KEGG HMM files in database directory. Please run VIBRANT_setup.py. And I have run python VIBRANT_setup.py -test and get VIBRANT v1.2.1 is good to go! See example_data/ for quick test files. in the log file. I tried to deal with it refering to issue 35 but it didn`t work.

[ZhengXiaoxuan11542]

I solved this issue by givening the database address mannually by -d. So far the programming is running successfully.

[AndAvia]

I solved this issue by givening the database address mannually by -d. So far the programming is running successfully.

老师您好，我设置数据库位置不成功，请问您是怎样设置的，这是我的代码及报错 VIBRANT_run.py -d ~/miniconda3/envs/VIBRANT/share/vibrant-1.2.0/databases

usage: VIBRANT_run.py [-h] [--version] -i I [-f {prot,nucl}] [-folder FOLDER] [-t T] [-l L] [-o O] [-virome] [-no_plot] [-d D] [-m M] VIBRANT_run.py: error: the following arguments are required: -i

[ZhengXiaoxuan11542]

我通过手动给出数据库地址解决了这个问题-d。至此编程运行成功。

老师您好，我设置数据库位置不成功，请问您是怎样设置的，这是我的代码及报错VIBRANT_run.py -d ~/ miniconda3/envs/VIBRANT/share/vibrant-1.2.0/databases

用法：VIBRANT_run.py [-h] [--version] -i I [-f {prot,nucl}] [-folder FOLDER] [-t T] [-l L] [-o O] [-virome] [-no_plot] [-d D] [-m M] VIBRANT_run.py：错误：需要以下参数：-i

Hi, Just command the database location when you run your programme. like VIBRANT_run.py -t 25 -l 5000 -i ~/yourname.fa -folder filter_location -d miniconda3/.../databases/

[AndAvia]

我通过手动给出的数据库地址解决了这个问题-d。直到此编程运行成功。

老师您好，我设置数据库位置不成功，请问您是怎样设置的，这是我的代码及报错VIBRANT_run.py -d ~/ miniconda3/envs/VIBRANT/share/vibrant-1.2.0/databases 用法：VIBRANT_run.py [-h] [--version] -i I [-f {prot,nucl}] [-folder FOLDER] [-t T] [-l L] [-o O] [-virome] [-no_plot] [-d D] [-m M] VIBRANT_run.py：错误：需要以下参数：-i

您好，只需在运行程序时命令数据库位置即可。喜欢VIBRANT_run.py -t 25 -l 5000 -i ~/yourname.fa -folder filter_location -d miniconda3/.../databases/

太感谢您了，运行成功了