Let’s create an interactive session on the HPC:
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qsub -I -S /bin/bash -l walltime=10:00:00 -l select=1:ncpus=2:mem=4gb |
Install tools using conda
Approach #1 - installing tools one at a time (faster option)
Create a conda environment called sniffles
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conda create -n ONTvariants_QC |
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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/ONTvariants_QC
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate ONTvariants_QC
#
# To deactivate an active environment, use
#
# $ conda deactivate |
Let’s activate the conda environment:
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conda activate ONTvariant_QC |
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:
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nanoplot, porechop_abi, chopper |
For example, search for nanoplot:
...
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conda install bioconda::nanoplot |