{"id":365,"date":"2013-04-26T12:57:36","date_gmt":"2013-04-26T12:57:36","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=365"},"modified":"2018-06-26T09:14:20","modified_gmt":"2018-06-26T09:14:20","slug":"perl","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/perl\/","title":{"rendered":"Perl"},"content":{"rendered":"

Overview<\/h2>\n

Perl is a programming language which is particularly good for text manipulation.<\/p>\n

Versions available: 5.10.1, 5.16.3, 5.20.1 and 5.20.2<\/p>\n

Bioperl 1.6.1 is included in the 5.16.3 install and later.<\/p>\n

Restrictions on use<\/h2>\n

Perl is open source. All users are able to access and use it.<\/p>\n

Set up procedure<\/h2>\n

The default version of Perl on the CSF is 5.10.1 – you do not need to load a modulefile to access it.<\/p>\n

To use version 5.20.2 please load the modulefile:<\/p>\n

\r\nmodule load apps\/gcc\/perl\/5.20.2\r\n<\/pre>\n
Running the application<\/h2>\n
Please do not run anything other than very short simple perl programs on the login node. All computational work must be run in batch. Please see the CSF SGE documentation<\/a> for example job submission scripts. <\/p>\n
Installing extra modules<\/h2>\n
If you try to run a Perl script and it fails to find a module, such as<\/p>\n
\r\nCan't locate Term\/ReadKey.pm in @INC ...\r\n<\/pre>\n
you can usually install the missing one in your home directory from the CPAN archive (unless what you’re running comes with specific different instructions).<\/p>\n
First you have to configure the cpan<\/code> command to install into your home directory if you haven’t done so before.  Run this and hit return at the prompt:<\/p>\n
\r\nperl -MCPAN -e 'mkmyconfig'\r\n<\/pre>\n
You also need environment variables to point to what you’ve configured.  To set that up conveniently, do the following (assuming you use the default shell):<\/p>\n
\r\neval $(perl -I$HOME\/perl5\/lib\/perl5 -Mlocal::lib)\r\n<\/pre>\n
You might want to add that line to your .bashrc<\/code> file for future use.<\/p>\n
Convert the file name from the error message into a module name by replacing \/<\/code> with ::<\/code>, and then install it similarly to (for the above case):<\/p>\n
\r\ncpan Term::ReadKey\r\n<\/pre>\n
Hit the return key at any prompts, and it should eventually install the new module under perl5<\/code> in your home directory.  The procedure may take a while and print lots.  The environment variable PERL5LIB<\/code> needs to be set to ~\/perl5\/lib\/perl5<\/code> to find it; the eval<\/code> step above does that.  You can install multiple modules by passing the names as arguments to cpan<\/code>, or just use cpan<\/code> multiple times.<\/p>\n
The installation procedure will only work on the login nodes, but you can use the result on compute nodes as long as PERL5LIB<\/code> is set correctly.  The installation will currently only work with the default Perl version, not the ones requiring modules; however, the result should be usable with other versions if the eval<\/code> step is done before loading the module.<\/p>\n
Further info<\/h2>\n