Difference between revisions of "HPC:Perl"
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+ | === Perl === | ||
Perl version 5.10.1 has been installed across the cluster, along with the popular BioPerl libraries. | Perl version 5.10.1 has been installed across the cluster, along with the popular BioPerl libraries. | ||
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export MANPATH=$PERL5LIB/man:$MANPATH | export MANPATH=$PERL5LIB/man:$MANPATH | ||
</pre> | </pre> | ||
+ | |||
+ | ==== Running Perl scripts non-interactively ==== | ||
+ | |||
+ | Shown below is a sample Perl script: | ||
+ | <pre> | ||
+ | $ cat simple.pl | ||
+ | #!/usr/bin/env perl | ||
+ | use warnings; | ||
+ | print "Hello!\n"; | ||
+ | </pre> | ||
+ | |||
+ | The above script can be run on the PMACS HPC cluster: | ||
+ | |||
+ | <pre> | ||
+ | $ bsub -e simple.e -o simple.o perl simple.pl | ||
+ | </pre> | ||
+ | |||
+ | === Other Pages === | ||
+ | ---- | ||
+ | <div class="mw-collapsible mw-collapsed"> | ||
+ | *[[HPC:FAQ|HPC FAQ ]] | ||
+ | *[[HPC:Login|Connecting to the PMACS cluster]] | ||
+ | *[[HPC:User_Guide|User Guide]] | ||
+ | *[[HPC:Software|Available Software]] | ||
+ | *[[HPC:Archive System|PMACS Archive System]] | ||
+ | </div> |
Latest revision as of 15:45, 13 August 2019
Contents
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