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Deatherage, Daniel E

Deatherage, Daniel E

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cpan module installations

Warning
titleAgain, make sure you are NOT on an idev node for working with cpan



If you attempt to launch cpan, you likely get a message similar to the following:

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Code Block
titleInstall Perl modules required for SVDetect. (I do not know why the words do and for are appearing in bold, they are not meant as some kind of hint).
# choose 'yes' to do as much automatically as possible 
# choose 'local::lib' for the approach you want (as you don't have admin rights on TACC)
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cpan[1]> # choose 'yes' to append the information to your .bashrc file
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cpan[1]> install Config::General
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cpan[2]> install Tie::IxHash
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cpan[3]> install Parallel::ForkManager
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cpan[4]> quit
Note
titleHow to fix cpan if downloads give errors

Several students were having trouble with the cpan downloads that seem to be related to some kind of interruption in the initial download process. The following commands have solved the issue for at least 1 student. Please try the following if you were unable to get the above cpan downloads to work, and let me know if you continue to experience difficulties.

Expand
Code Block
languagebash
titlerelaunch cpan
/bin/cpan
Code Block
languagebash
titleOn the cpan prompt
o conf init

This should then get you back to the point where you can:

Code Block
titleInstall Perl modules required for SVDetect. (I do not know why the words do and for are appearing in bold, they are not meant as some kind of hint).
# choose 'yes' to do as much automatically as possible 
# choose 'local::lib' for the approach you want (as you don't have admin rights on TACC)
# choose 'yes' to append the information to your .bashrc file
...
cpan[1]> install Config::General
...
cpan[2]> install Tie::IxHash
...
cpan[3]> install Parallel::ForkManager
...
cpan[4]> quit

The above solution is based on steps 4-7 of this page. Again, if this does not fix the problem you were having, please let me know.

Info
titleWhy we choose "yes" to append information to our .bashrc file.

Just before getting your cpan prompt, there is a block of text that looks something like this

No Format
PATH="/home1/0004/train402/perl5/bin${PATH:+:${PATH}}"; export PATH;
PERL5LIB="/home1/0004/train402/perl5/lib/perl5${PERL5LIB:+:${PERL5LIB}}"; export PERL5LIB;
PERL_LOCAL_LIB_ROOT="/home1/0004/train402/perl5${PERL_LOCAL_LIB_ROOT:+:${PERL_LOCAL_LIB_ROOT}}"; export PERL_LOCAL_LIB_ROOT;
PERL_MB_OPT="--install_base \"/home1/0004/train402/perl5\""; export PERL_MB_OPT;
PERL_MM_OPT="INSTALL_BASE=/home1/0004/train402/perl5"; export PERL_MM_OPT;

Would you like me to append that to /home1/0004/train402/.bashrc now? [yes]

The answer here is yes. What is being asked is if you would like the computer by default to be able to access these new perl 'lib' (libraries) you have created, and if you want perl binaries in your PATH. Recall that the PATH variable is where the command line searches when you enter a command so that you don't have to specify its location from the root directory. Similar is true of the PERL_LOCAL_LIB_ROOT and other variables except instead of being searched from the command line, the perl program searches them when commands inside the perl script are accessed. While there are ways to specify how to access these libraries when running individual commands, that is going to be much more complicated at a minimum, and may require editing scripts or programs.


Once you quit cpan, you will get a message to restart your shell. Since you are on a remote computer, you can accomplish the same thing by logging out of TACC and sshing back in.

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