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Install tools using conda

Create a conda environment called sniffles

conda create -n sniffles
Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.5.0

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /home/barrero/miniconda3/envs/sniffles



Proceed ([y]/n)? 

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate sniffles
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Let’s activate the conda environment:

conda deactivate

Next, we need to install few tools for today’s exercises. Now let’s go the https://anaconda.org and search for the following tools and instructions on how to install them:

minimap2, samtools, sniffles

For example, search for the aligner minimap2:

image-20240515-212339.png

If the tool you are looking is available in conda, a list of options will be presented. Typically choose the option at the top with most downloads and compatible for your system:

image-20240515-212540.png

Click on the link to the tool of interest and you will be presented with the conda command line to run in your system to install the tool:

image-20240515-212825.png

  1. activate the conda environment

conda activate pvirdb

(optional) then prepare the following environment.yml file or go to step 3

name: pvirdb
channels:
  - conda-forge
  - defaults
dependencies:
  - bottleneck=1.3.5=py37h3a130e4_0
  - ca-certificates=2022.6.15=h5b45459_0

Update current environment

conda env update --file environment.yml

or create a new environment using this file

conda env create -f environment.yml

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