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avierstr / amplicon_sorter

Sorts amplicons from Nanopore sequencing data based on similarity
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amplicon_sorter on Conda #1

Open leocaserta opened 4 years ago

leocaserta commented 4 years ago

Hello Do you have plans to make amplicon_sorter available to install by Conda? It would be great if it was available as a package with all dependencies, i am having some trouble to install some of these dependencies.

avierstr commented 4 years ago

Hi Leocaserta, I'll try to get that done, but that is new for me and for the moment I'm getting a lot of errors in the process of making it conda-build. What problems do you have to install the dependencies ?

leocaserta commented 4 years ago

I've just realized that python3 was already installed in the cloud, amplicon_sorter is working now.
I have other questions about the results but i will create a new issue.

Thank you

Koen-vdl commented 1 year ago

Hi @avierstr,

Feel like your installation instructions might represent a barrier to new users who wish to try your promising tool out. You can create an easy conda env for amplicon_sorter using:

conda create -n ampliconsorter_env matplotlib biopython python-edlib python=3.6
conda activate ampliconsorter_env 
wget https://raw.githubusercontent.com/avierstr/amplicon_sorter/master/amplicon_sorter.py
python amplicon_sorter.py --help
avierstr commented 1 year ago

Thanks @Koen-vdl, I'll try that and add it to the information to install or use it.

hvbakel commented 1 year ago

Dear @avierstr, I recently started using amplicon_sorter and it fits our use-case perfectly. Happy to help set up a conda-build recipe to build a conda package for the script.

avierstr commented 12 months ago

Dear @hvbakel, I keep postponing that because I'm working on something else for the moment. I have not even tried Koen-vdl his suggestion yet... All help or advice on that is welcome.

ocstringham commented 8 months ago

Hi @avierstr,

Feel like your installation instructions might represent a barrier to new users who wish to try your promising tool out. You can create an easy conda env for amplicon_sorter using:

conda create -n ampliconsorter_env matplotlib biopython python-edlib python=3.6
conda activate ampliconsorter_env 
wget https://raw.githubusercontent.com/avierstr/amplicon_sorter/master/amplicon_sorter.py
python amplicon_sorter.py --help

There are some problems with installing edlib in conda: https://github.com/Martinsos/edlib/issues/151. I just removed that from the conda create then once env is activated I ran pip install edlib and amplicon_sorter runs:

conda create -n ampliconsorter_env matplotlib biopython python-edlib python=3.8
conda activate ampliconsorter_env 
pip install edlib
wget https://raw.githubusercontent.com/avierstr/amplicon_sorter/master/amplicon_sorter.py
python amplicon_sorter.py --help