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Jit published a blog post How to install Perl modules manually, using CPAN command, and other quick ways in the group Perl *PIPERsComments- BioStar 1330 days ago
To install BioPerl on a macOS system, you can follow these steps:
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Open the Terminal app on your macOS system.
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Install Homebrew if you haven't already installed it by entering the following command:
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)" -
Update Homebrew by entering the following command:
brew update -
Install Perl by entering the following command:
brew install perl -
Install cpanminus by entering the following command:
brew install cpanminus -
Install BioPerl by entering the following command:
cpanm BioPerl -
Verify the installation by running a BioPerl script or entering the following command to check the BioPerl version:
perl -MBio::Perl -e 'print "$Bio::Perl::VERSION\n"'
If there are any issues with the installation, you can try searching for solutions online or consulting the BioPerl documentation.
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- BioStar 1324 days ago
Installing in CONDA env
You can check using
which perl- it should give you the perl that's located within your conda environment. In this case, it should install things into your conda-directory.When you install packages via cpan it will also print the folder perl is installing the package into.
If you want to be extra-sure, you can also install most Perl packages via conda. Replace the ':' by '-', lower-case everything, and add 'perl-' to the beginning. In your case,
conda install -c bioconda perl-lwp-simplethis will definitely install into conda.
- BioStar 1324 days ago
If using conda
conda create --name perlENV perl
conda activate perlENVconda install -c bioconda perl-bundle-bioperl
conda install -c bioconda perl-bioperl
- Archana Malhotra answered the question What a bioinformatician should must know ?
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- Rahul Agarwal 4738 days ago
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- Radha Agarkar 4738 days ago
Recently published Nature commentary on "So you want to be a computational biologist?" by Nick Loman & Mick Watson give advice when starting out on computational projects. http://www.nature.com/nbt/journal/v31/n11/full/nbt.2740.html
- Archana Malhotra published a news post Bioinformatics: Introduction to PERL in the group Perl *PIPERsComments
- Jitendra Narayan 4828 days ago
Thanks Archana for such a useful links. I found this link useful as well for beginners, where user can find some of the free books.
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