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KennthShang / PhaBOX

Local version of the virus identification and analysis web server (tool set)
https://phage.ee.cityu.edu.hk/
Academic Free License v3.0
37 stars 5 forks source link

Can this tool be directly installed through conda? #18

Closed iquasere closed 1 month ago

iquasere commented 4 months ago

Hello,

I am interested in using this tool, and integrating it in a snakemake pipeline. However, the steps detailed in the README complicate the integration of the tool, since the paths have to be known before hand, and the name of the environment will be unpredictable (since it is a conda environment created by snakemake).

I want to know if it is possible to install this tool through something like conda install phabox. If not, can it be installed through pip?

KennthShang commented 4 months ago

I think you refer to the part of moving "blastxml_to_tabular.py" to the conda env?

Sorry for the confusion. We just forgot to remove that description, and it is useless for the current version by using the --script option. For the installation, you only need to runconda env create -f webserver.yml -n phabox once.

BTW, We will consider the binary usage installation in the near further and update the program soon. Thanks.

Best, Jiayu

joao1980 commented 3 months ago

Hi, I would also be interested in having a conda package ready to go for the tool. :) In my case I am using nextflow. Best, Joao

KennthShang commented 3 months ago

Hi there,

We have made an update and the packages can be installed via:

conda create -n PhaBOX phabox=1.1 -c bioconda -c conda-forage -c pytorch -c jyshang2

Or 

conda create -n ENV_NAME python=3.9.7
conda activate ENV_NAME
conda install phabox=1.1 -c bioconda -c conda-forage -c pytorch -c jyshang2

Best, Jiayu

KennthShang commented 1 month ago

Hi there,

The PhaBOX is upgraded to a 2.0 version with more powerful usage. Besides, it can handle all kinds of viruses now. Feel free to check!

Best, Jiayu