[Bioperl-l] bioperl on CentOS 6.4

Fields, Christopher J cjfields at illinois.edu
Wed Nov 20 18:03:40 UTC 2013

Re: Test::Most, you only need this if you intend on testing the distribution.  If so, you will need to build it; it is a convenience module that encompasses all the various Test::* modules we use (Test::More, Test::Warn, etc.)

We have a number of users using either CentOS/RHEL (we have both Debian and CentOS/RHEL locally).  In general we avoid messing with the system (RHEL-specific) perl when possible, in preference for installing a local perl version that we can easily update if needed.  This completely depends on your needs of course, but if the intent of using RPMs is to make (un)installation/upgrades easier for perl modules, just want to point out other packaging options like pinto or stratopan (http://perltricks.com/article/48/2013/11/15/A-Stratopan-quick-start-user-guide).  I believe that is thanks to the folks at genentech.

Also, we do intend on splitting out modules with dependencies so this process will become a little easier hopefully, but I only have so much time I can invest these days towards this end.  So, any help is greatly appreciated.


On Nov 20, 2013, at 10:50 AM, m.roth at 5-cent.us wrote:

> Ok, I'm going to try 1.6.922 again. I've d/l it, and, like the former, has
> files in it with perl in /bin and /usr/local/bin. The 1.6.901 patch I have
> has a problem; I d/l the debian patch file, and used it.
> However... I have no such perl module pacakge as perl-Test-Most. Is there
> something else I can patch this with, or is that another prerequisite I
> have to build?
> As I noted originally, there are things that 1.6.922 wants that I don't
> have. I've already built half a dozen other things, like
> monkres::algorithm, and Stag, etc.
> IS anyone on the list running BioPerl on any RHEL or RHEL-descended system?
>        mark
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