HPC:Perl
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Revision as of 15:45, 13 August 2019 by Obki (talk | contribs) (→Running Perl scripts non-interactively)
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Perl
Perl version 5.10.1 has been installed across the cluster, along with the popular BioPerl libraries.
User installed Perl Modules from CPAN using CPAN Minus
CPAN Minus is a light-weight replacement for CPAN. In order to install your own Perl modules, you can use the CPAN Minus tool (cpanm) with the --local-lib option:
[asrini@node063 ~]$ cpanm --help
Usage: cpanm [options] Module [...]
Options:
-v,--verbose Turns on chatty output
-q,--quiet Turns off the most output
--interactive Turns on interactive configure (required for Task:: modules)
-f,--force force install
-n,--notest Do not run unit tests
--test-only Run tests only, do not install
-S,--sudo sudo to run install commands
--installdeps Only install dependencies
--showdeps Only display direct dependencies
--reinstall Reinstall the distribution even if you already have the latest version installed
--mirror Specify the base URL for the mirror (e.g. http://cpan.cpantesters.org/)
--mirror-only Use the mirror's index file instead of the CPAN Meta DB
--prompt Prompt when configure/build/test fails
-l,--local-lib Specify the install base to install modules
-L,--local-lib-contained Specify the install base to install all non-core modules
--auto-cleanup Number of days that cpanm's work directories expire in. Defaults to 7
Commands:
--self-upgrade upgrades itself
--info Displays distribution info on CPAN
--look Opens the distribution with your SHELL
-V,--version Displays software version
Examples:
cpanm Test::More # install Test::More
cpanm MIYAGAWA/Plack-0.99_05.tar.gz # full distribution path
cpanm http://example.org/LDS/CGI.pm-3.20.tar.gz # install from URL
cpanm ~/dists/MyCompany-Enterprise-1.00.tar.gz # install from a local file
cpanm --interactive Task::Kensho # Configure interactively
cpanm . # install from local directory
cpanm --installdeps . # install all the deps for the current directory
cpanm -L extlib Plack # install Plack and all non-core deps into extlib
cpanm --mirror http://cpan.cpantesters.org/ DBI # use the fast-syncing mirror
You can also specify the default options in PERL_CPANM_OPT environment variable in the shell rc:
export PERL_CPANM_OPT="--prompt --reinstall -l ~/perl --mirror http://cpan.cpantesters.org"
Type `man cpanm` or `perldoc cpanm` for the more detailed explanation of the options.
[asrini@node063 ~]$ cpanm -l perl5 Astro::Time
--> Working on Astro::Time
Fetching http://www.cpan.org/authors/id/C/CP/CPHIL/Astro-0.75.tar.gz ... OK
Configuring Astro-0.75 ... OK
Building and testing Astro-0.75 ... OK
Successfully installed Astro-0.75
1 distribution installed
[asrini@node063 ~]$ tree perl5/
perl5/
├── lib
│ └── perl5
│ ├── Astro
│ │ ├── Coord.pm
│ │ ├── Misc.pm
│ │ └── Time.pm
│ └── x86_64-linux-thread-multi
│ ├── auto
│ │ └── Astro
│ └── perllocal.pod
└── man
└── man3
├── Astro::Coord.3pm
├── Astro::Misc.3pm
└── Astro::Time.3pm
8 directories, 7 files
Installing other perl tools not in CPAN
Refer to the tool's documentation, but usually you supply a PREFIX or INSTALL_BASE to perl Makefile.PL.
Configuring your Perl environment to use local Modules
In order to take advantage of these modules and manpages, you will need define a directory to install them to as well as set a proper value for PERL5LIB.
To define the proper environment variables, you can use the perl5lib environment module:
# add to .bashrc or .tchsrc file module load perl5lib
Alternatively, you can put the following in your .bashrc file:
export PERL5LIB=~/perl5/ export PATH=$PERL5LIB/bin:$PATH export MANPATH=$PERL5LIB/man:$MANPATH
Running Perl scripts non-interactively
Shown below is a sample Perl script:
$ cat simple.pl #!/usr/bin/env perl use warnings; print "Hello!\n";
The above script can be run on the PMACS HPC cluster:
$ bsub -e simple.e -o simple.o perl simple.pl
