Following this tutorial and two installation steps, I want to run SimLoRD.
On Ubuntu 18.04, using a Python 3.9 venv:
conda install -c bioconda simlord
UnsatisfiedError
I have tried this on Windows and Linux with different versions of Anaconda and Python without luck.
Suggested pip install simlord==1.0.4 via. Windows 10:
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
Hello,
Python 3.9 has few major changes and might not be supported. So maybe trying python version 3.6 might have luck. This is likely the issue in your case. There are several breaking changes with python 3.9/3.8.
conda create --name simlord_env python=3.6.5
Then activate the environment.
conda activate simlord_env
Now install simlord using the command;
conda install -c bioconda simlord
This way simlord command will be available whenever simlord_env is active in your terminal.
Hi, so much appeared to work in Terminal that didn't before but ultimately I still landed with the same error on Windows CMD. I will try after 9am (BST) on my Linux VM on my uni servers
Thank you so much. I have it installed now. Am I correct in saying that SimLoRD works with only .fasta files, creates a .fastq file and then you can vectorise it?
I've learnt since that Vectorisation is a different process. It's Computer Science, where data is represented as probabilistic decimal numbers. It's used for various computations, such as Cluster Analysis.
Please use conda to install bioinformatics software. You will save on asking a lot of questions. Use conda part of the tutorial: Creating workflows with snakemake and conda
Then it can be as simple as:
conda create -n ea-utils ea-utils
conda activate ea-utils
BTW: Why do you want to specifically use ea-utils? It is older software and there may be other more current options that you can/should use instead.
Will do. My mission is to get read files from .fastq files of which I already have. Thank you for your responses.
Sorry, I meant reads; not 'read files'. I am following this TDS tutorial https://towardsdatascience.com/composition-based-clustering-of-metagenomic-sequences-4e0b7e01c463. Here they describe extracting reads from a .fastq file. The tutorial in the post shows how to do so with ea-utils.
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Both Windows and Linux Ubuntu have struggled working with the conda command
Struggled in what way?
It is critical that the order of repositories be exactly as shown here. Execute these commands again to be sure.
You have to keep in mind that not every bioinformatics package is going to be available in conda. It the issue has been with the speed of
resolutionof package names then there is a better way to do that usingmamba. If you feel comfortable withcondathen try this: Greatly speed up conda by using mambaIt keeps saying command not found :( I really am trying
If you used
minicondato installcondathen it is likely present in this directory$HOME/miniconda3/condabin/conda. Check to make sure you see it there byls -l $HOME/miniconda3/condabin/conda. If that shows a result then doexport PATH=$PATH:$HOME/miniconda3/condabin/. This will allow you to runcondaseamlessly.It would help to get some command line basics under you belt. I recommend this online tutorial for basic unix.
I used Anaconda 3. I now have Python 3.9 as my venv. but still get UnsatisfiableError.
Don't create separate venv in python. Allow
condato create a new environment for packages and it will install all necessary dependencies in it. When you activate that environment (conda activate) you will be able to use those programs.If you used
anacondathen yourcondais likely in$HOME/anaconda/bin/conda. In that case you will doexport PATH=$PATH:$HOME/anaconda/bin/.