perl

[William H. Magill]

> You do not need to know Perl to run Circos. You do need to be familiar with:
> 
> 	• concept of directories and files
> 	• navigating directories at the command prompt
> 	• creating and deleting directories at the command prompt
> 	• concept of absolute and relative paths 
> Well I can do that, I have done that:)

The following may be a bit esoteric, but has proved to be a "gotcha" more than one time 
when "porting" software from a Unix like environment (i.e. various LINUX variants)  to OSX.
(And, being retired, I'm now a bit rusty at this, so hopefully others will correct anything I've
misstated or mis-remembered. And I don't know Circos at all.)

One thing which has not been mentioned so far, but which is "assumed" -- 
that you understand the concept of "path" under OSX. It is slightly different compared to Linux!
(I.e. whose "PATH" is used, and  when -- and where it is set.)

MacPorts installs (modifies) your path environment variable in your .profile to include MacPorts
"paths" ahead of system paths.

<----------- example ------------->
# MacPorts Installer addition on 2011-10-02_at_12:10:51: adding an appropriate PATH variable for use with MacPorts.
export PATH=/opt/local/bin:/opt/local/sbin:$PATH
export INFOPATH=/opt/local/share/info:/usr/share/info:$INFOPATH
# Finished adapting your PATH environment variable for use with MacPorts.
<----------- end example ------------->

First thing to note is that the MacPorts installation modification ONLY modifies $PATH and $INFOPATH
It does not modify $LD_LIBRARY_PATH.
Historically, this has not been a problem, however there are "things out there" which expect
that information for one reason or another. (I have no idea if Circos is one of "them.")

Because of changes Apple has made in OSX 10.8 (Mountain Lion), the main thing to be aware of is that
this .profile file is ONLY executed automatically from the command line for items launched from within a 
Terminal session initiated from your  "login window."

Previous versions of OSX used the file: ~/.MacOSX/environment.plist as a mechanism to pass this same
information on to programs which WERE NOT LAUNCHED DIRECTLY FROM YOUR TERMINAL WINDOW,
but which ran under your userid. 
That is, programs configured to "auto-start" from things like cron or your login window.


T.T.F.N.
William H. Magill
# iMac11,3 Core i7 [2.93GHz - 8 GB 1067MHz] OS X 10.8.2
# MacBook Pro4.1 Core 2 Duo [2.5GHz - 4GB 667] OS X 10.6.8
# Macmini6,1 Intel Core i5 [2.5 Ghz - 4GB 1600MHz] OS X 10.8.2

magill at mac.com
whmagill at gmail.com