conda install -c bioconda simlord | SimLoRD

Question

[Anonymous]

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

Terminal output

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.

Windows pip install error

[Anonymous]

Both Windows and Linux Ubuntu have struggled working with the conda command

[GenoMax]

Struggled in what way?

It is critical that the order of repositories be exactly as shown here. Execute these commands again to be sure.

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

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 resolution of package names then there is a better way to do that using mamba. If you feel comfortable with conda then try this: Greatly speed up conda by using mamba

[Anonymous]

It keeps saying command not found :( I really am trying

[GenoMax]

If you used miniconda to install conda then it is likely present in this directory $HOME/miniconda3/condabin/conda. Check to make sure you see it there by ls -l $HOME/miniconda3/condabin/conda. If that shows a result then do export PATH=$PATH:$HOME/miniconda3/condabin/. This will allow you to run conda seamlessly.

It would help to get some command line basics under you belt. I recommend this online tutorial for basic unix.

[Anonymous]

I used Anaconda 3. I now have Python 3.9 as my venv. but still get UnsatisfiableError.

[GenoMax]

Don't create separate venv in python. Allow conda to 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 anaconda then your conda is likely in $HOME/anaconda/bin/conda. In that case you will do export PATH=$PATH:$HOME/anaconda/bin/.

Answer 1

[anuradhawick]

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.

[Anonymous]

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

[Anonymous]

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?

[GenoMax]

Correct up to .fastq part. I am not sure what you mean by vectorize. You simply have a simulated fastq file that has real fastq sequence data. It can be used for any analysis that you normally would do with real data.

[Anonymous]

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.

Answer 2

[GenoMax]

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.

[Anonymous]

Will do. My mission is to get read files from .fastq files of which I already have. Thank you for your responses.

[GenoMax]

Fastq files are plain text. What do you mean by get read files from .fastq files? You can simply look at contents of an uncompressed fastq file using less/cat/more command.

[Anonymous]

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.