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4. Easy Installation

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gitarunprasanna83 edited this page Aug 17, 2019 · 2 revisions

Anaconda for life !

Conda makes your life very easy ! Most of the bio-packages are now distributed in conda. You can create multiple virtual environments, which allows easy 1 command installation, solves version conflicts etc.,

Download and install anaconda from (Prefer Python 3x)

Anaconda_download

After GUI-based installation,

  1. Create an environment

conda_env

  1. Activate an environment

conda_activate

  1. Install a software: type conda install -c bioconda seqkit

conda_install

  1. Go to the folder where, you have genome and protein file and type:

seqkit stats *.fa

Explore the other utilities of seqkit !

  1. To exit the environment, use conda deactivate

Small Assignment

  1. Create a conda environment named "Samtools"

  2. Install samtools through bioconda channel

  3. Activate the environment

  4. type samtools faidx E.coli_genome.fa (remember the genome fasta file)

  5. Download and install IGV "IGV viewer"

  6. Load the genome file using "Genomes" tab

  7. Load the gff file using "File" tab

  8. Can you see this ?

IGV_Viewer

Summary:

Now you know how to install packages related to bioinformatics in hassle-free method !

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