BOL: Installing Perl environment on Linux

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Installing Perl environment on Linux

Installing Perl environment on Linux

By using plenv, you can easily install and switch among different version of Perl. This will be installed under your home directory in~/.plenv.

Install latest Perl (with supporting multithreading) and CPANMinus.

 $ cd
 $ git clone git://github.com/tokuhirom/plenv.git ~/.plenv
 $ git clone git://github.com/tokuhirom/Perl-Build.git ~/.plenv/plugins/perl-build/
 $ echo 'export PATH="$HOME/.plenv/bin:$PATH"' >> ~/.bashrc
 $ echo 'eval "$(plenv init -)"' >> ~/.bashrc
 $ source ~/.bashrc
 $ plenv install 5.18.1 -Dusethreads
 $ plenv rehash
 $ plenv global 5.18.1
 $ plenv install-cpanm

git is a distributed revision control and source code management software which can help you to download files from GitHub server.
echo means "print".
>> means adding the output into the end of the file, while > means adding the output by overwriting the whole file. Please use> with additional cares.
In Linux system, there are two types of outputs when you execute a command. One is called standard output (or sometimes STDOUT for short), and the other is a standard error (STDERR). 1> is for STDOUT only, 2> is for STDERR only, and &>means for both. In default > is the same to 1>.
exec is execution.
Remember to install Perl in supporting multithreading (with option -Dusethreads), which is important for many NGS analysis packages (e.g. Trinity). In this setting, you can use multiple CPU for Perl software.
Install the CPAN (Comprehensive Perl Archive Network) manager software, CPANMinus, by install-cpanm.

You can use plenv global and plenv local to change the different version of Perl to fulfil different needs of your Perl software.

For example, if the specific version of Perl is not compatible with your script, you can switch to the different version by:

 $ plenv local

It is similar to set the local version of your script language when you use pyenv and rbenv as the following.

Put the following path into ~/.bashrc file.

export PERL5LIB="$HOME/.plenv/build/perl-5.18.1/lib"

Install BioPerl and PerlIO::gzip

CPANMinus is a very good Perl module manager, use cpanm to install BioPerl can save you a lot of time. Here are some useful modules:

$ cpanm Bio::Perl
$ cpanm Bio::SearchIO
$ cpanm PerlIO::gzip

For more information, please visit: https://github.com/tokuhirom/plenv

Comments

- Jit@jit.aber
Jit 2358 days ago
curl -L http://cpanmin.us | perl - --sudo App::cpanminus

The above is installing the "zero configuration CPAN modules installer" called cpanm. (Can take several minutes to install - don't break the process)
and after - simply:
cpanm Foo cpanm Module::One cpanm Another::Module
- Jit@jit.aber
Jit 2358 days ago
If Conda is installed

➜ parallelLastz git:(master) ✗ conda create -n myLocalPerl perl perl-app-cpanminus
Solving environment: done
## Package Plan ##
environment location: /home/urbe/anaconda3/envs/myLocalPerl
added / updated specs:
- perl
- perl-app-cpanminus

The following packages will be downloaded:
package | build
---------------------------|-----------------
perl-threaded-5.22.0 | 10 11.2 MB bioconda
perl-app-cpanminus-1.7039 | 2 220 KB bioconda
------------------------------------------------------------
Total: 11.4 MB
The following NEW packages will be INSTALLED:
libgcc: 7.2.0-h69d50b8_2
libgcc-ng: 7.2.0-hdf63c60_3
libstdcxx-ng: 7.2.0-hdf63c60_3
perl: 5.26.2-h470a237_0 conda-forge
perl-app-cpanminus: 1.7039-2 bioconda
perl-threaded: 5.22.0-10 bioconda
Proceed ([y]/n)? Y

Downloading and Extracting Packages
perl-threaded-5.22.0 | 11.2 MB | ############################################### | 100%
perl-app-cpanminus-1 | 220 KB | ############################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use:
# > source activate myLocalPerl
#
# To deactivate an active environment, use:
# > source deactivate
#
➜ parallelLastz git:(master) ✗ source activate myLocalPerl
(myLocalPerl) ➜ parallelLastz git:(master) ✗ cpanm Parallel::ForkManager
--> Working on Parallel::ForkManager
Fetching http://www.cpan.org/authors/id/Y/YA/YANICK/Parallel-ForkManager-1.19.tar.gz ... OK
Configuring Parallel-ForkManager-1.19 ... OK
==> Found dependencies: Test::Warn
--> Working on Test::Warn
Fetching http://www.cpan.org/authors/id/B/BI/BIGJ/Test-Warn-0.36.tar.gz ... OK
Configuring Test-Warn-0.36 ... OK
==> Found dependencies: Sub::Uplevel
--> Working on Sub::Uplevel
Fetching http://www.cpan.org/authors/id/D/DA/DAGOLDEN/Sub-Uplevel-0.2800.tar.gz ... OK
Configuring Sub-Uplevel-0.2800 ... OK
Building and testing Sub-Uplevel-0.2800 ... OK
Successfully installed Sub-Uplevel-0.2800
Building and testing Test-Warn-0.36 ... OK
Successfully installed Test-Warn-0.36
Building and testing Parallel-ForkManager-1.19 ... OK
Successfully installed Parallel-ForkManager-1.19
3 distributions installed
(myLocalPerl) ➜ parallelLastz git:(master) ✗ perl parallelLastz.pl
Can't locate Bio/SeqIO.pm in @INC (you may need to install the Bio::SeqIO module) (@INC contains: /home/urbe/perl5 /home/urbe/anaconda3/envs/myLocalPerl/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/urbe/anaconda3/envs/myLocalPerl/lib/site_perl/5.26.2 /home/urbe/anaconda3/envs/myLocalPerl/lib/5.26.2/x86_64-linux-thread-multi /home/urbe/anaconda3/envs/myLocalPerl/lib/5.26.2 .) at parallelLastz.pl line 10.
BEGIN failed--compilation aborted at parallelLastz.pl line 10.
(myLocalPerl) ➜ parallelLastz git:(master) ✗ cpanm Bio::SeqIO
--> Working on Bio::SeqIO
Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.007002.tar.gz ... OK
==> Found dependencies: Module::Build
--> Working on Module::Build
Fetching http://www.cpan.org/authors/id/L/LE/LEONT/Module-Build-0.4224.tar.gz ... OK
Configuring Module-Build-0.4224 ... OK
Building Module-Build-0.4224 ... OK
Successfully installed Module-Build-0.4224
Configuring BioPerl-1.007002 ... OK
==> Found dependencies: Data::Stag, URI::Escape, IO::String, Test::Most
--> Working on Data::Stag
Fetching http://www.cpan.org/authors/id/C/CM/CMUNGALL/Data-Stag-0.14.tar.gz ... OK
Configuring Data-Stag-0.14 ... OK
==> Found dependencies: IO::String
--> Working on IO::String
Fetching http://www.cpan.org/authors/id/G/GA/GAAS/IO-String-1.08.tar.gz ... OK
Configuring IO-String-1.08 ... OK
Building and testing IO-String-1.08 ... OK
Successfully installed IO-String-1.08
Building and testing Data-Stag-0.14 ... OK
Successfully installed Data-Stag-0.14
--> Working on URI::Escape
Fetching http://www.cpan.org/authors/id/E/ET/ETHER/URI-1.74.tar.gz ... OK
Configuring URI-1.74 ... OK
==> Found dependencies: Test::Needs
--> Working on Test::Needs
Fetching http://www.cpan.org/authors/id/H/HA/HAARG/Test-Needs-0.002005.tar.gz ... OK
Configuring Test-Needs-0.002005 ... OK
Building and testing Test-Needs-0.002005 ... OK
Successfully installed Test-Needs-0.002005
Building and testing URI-1.74 ... OK
Successfully installed URI-1.74
--> Working on Test::Most
Fetching http://www.cpan.org/authors/id/O/OV/OVID/Test-Most-0.35.tar.gz ... OK
Configuring Test-Most-0.35 ... OK
==> Found dependencies: Test::Deep, Exception::Class, Test::Exception, Test::Differences
--> Working on Test::Deep
Fetching http://www.cpan.org/authors/id/R/RJ/RJBS/Test-Deep-1.128.tar.gz ... OK
Configuring Test-Deep-1.128 ... OK
Building and testing Test-Deep-1.128 ... OK
Successfully installed Test-Deep-1.128
--> Working on Exception::Class
Fetching http://www.cpan.org/authors/id/D/DR/DROLSKY/Exception-Class-1.44.tar.gz ... OK
Configuring Exception-Class-1.44 ... OK
==> Found dependencies: Devel::StackTrace, Class::Data::Inheritable
--> Working on Devel::StackTrace
Fetching http://www.cpan.org/authors/id/D/DR/DROLSKY/Devel-StackTrace-2.03.tar.gz ... OK
Configuring Devel-StackTrace-2.03 ... OK
Building and testing Devel-StackTrace-2.03 ... OK
Successfully installed Devel-StackTrace-2.03
--> Working on Class::Data::Inheritable
Fetching http://www.cpan.org/authors/id/T/TM/TMTM/Class-Data-Inheritable-0.08.tar.gz ... OK
Configuring Class-Data-Inheritable-0.08 ... OK
Building and testing Class-Data-Inheritable-0.08 ... OK
Successfully installed Class-Data-Inheritable-0.08
Building and testing Exception-Class-1.44 ... OK
Successfully installed Exception-Class-1.44
--> Working on Test::Exception
Fetching http://www.cpan.org/authors/id/E/EX/EXODIST/Test-Exception-0.43.tar.gz ... OK
Configuring Test-Exception-0.43 ... OK
Building and testing Test-Exception-0.43 ... OK
Successfully installed Test-Exception-0.43
--> Working on Test::Differences
Fetching http://www.cpan.org/authors/id/D/DC/DCANTRELL/Test-Differences-0.64.tar.gz ... OK
Configuring Test-Differences-0.64 ... OK
==> Found dependencies: Capture::Tiny, Text::Diff
--> Working on Capture::Tiny
Fetching http://www.cpan.org/authors/id/D/DA/DAGOLDEN/Capture-Tiny-0.48.tar.gz ... OK
Configuring Capture-Tiny-0.48 ... OK
Building and testing Capture-Tiny-0.48 ... OK
Successfully installed Capture-Tiny-0.48
--> Working on Text::Diff
Fetching http://www.cpan.org/authors/id/N/NE/NEILB/Text-Diff-1.45.tar.gz ... OK
Configuring Text-Diff-1.45 ... OK
==> Found dependencies: Algorithm::Diff
--> Working on Algorithm::Diff
Fetching http://www.cpan.org/authors/id/T/TY/TYEMQ/Algorithm-Diff-1.1903.tar.gz ... OK
Configuring Algorithm-Diff-1.1903 ... OK
Building and testing Algorithm-Diff-1.1903 ... OK
Successfully installed Algorithm-Diff-1.1903
Building and testing Text-Diff-1.45 ... OK
Successfully installed Text-Diff-1.45
Building and testing Test-Differences-0.64 ... OK
Successfully installed Test-Differences-0.64
Building and testing Test-Most-0.35 ... OK
Successfully installed Test-Most-0.35
Building and testing BioPerl-1.007002 ... OK
Successfully installed BioPerl-1.007002
16 distributions installed
- Jit@jit.aber
Jit 2358 days ago
You migth need to install this
sudo conda install -c bioconda perl-app-cpanminus

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Installing Perl environment on Linux

Install latest Perl (with supporting multithreading) and CPANMinus.

Install BioPerl and PerlIO::gzip

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