[Bioperl-l] help (fwd)

[Jason Stajich]

---------- Forwarded message ----------
Date: Thu, 02 Oct 2003 18:47:46 +0200
From: "[iso-8859-1] Antonio Ramos Fernández" <tniram at hotmail.com>
Subject: help

Help ! Help please !

Sorry about this question (it could seem some silly)  but I have some doubts
about bioperl installation and I don’t know anybody who could help me (I’ve
read the installation info at README, INSTALL, INSTALL_WIN, and bptutorial
core documentation files, but i think it’s not clear enough for me). I have
downloaded the zip-compressed 1.2.3 bioperl release, and my Win98 has the
5.8.0 Activestate Perl binary distribution installed. I have unzipped the
file and the directory tree is intact. I guess I have to move the “Bio”
folder to c:\perl\lib (I’ve read in INSTALL_WIN that the other stuff is
useful but not recommended to install). To install it, I understand I have
to execute the makefile.pl script, but if i move it out its original folder
it gives error messages about “tests”. If I move the full content of the
zip.file (decompressed) ot the c:\perl\lib folder makefile.pl runs and
prints info about external module requirements for some of the bioperl
modules (and does not seem to do anythhing else). It also prints:

Enjoy the rest of bioperl, which you can use after going 'make install'
Writing Makefile for Bio

I dont’ understand the steps I have to follow to install bioperl. MS-DOS
does not recognise these commands (I refer to the three steps make- make
install-make tests) and makefile.pl does not run without other files in the
zip “root directory”. I don’t know what I have to do exactly with the zip
content. I don’t remember all the command combinations and folders I’ve
tested, but I’ve noticed I don’t know what the hell I’m doing. I think three
new files have appeared in the perl\lib folder after running makefile.pl:
”bioperl.conf”,  “makefile” and “&1” (have I to erase them to try again?
-I’ve removed the bio folder from perl\lib after getting tired of all this).
Perl only notices the presence o specific modules when I include in my
scripts the statement [ use lib ‘c:\perl\lib\bio\module_name’;   ], but I
don’t think this is the best way to use the modules. Sorry, I started with
perl some months ago and I’m not a skilled programmer (and I have never been
the best friend of my computer). Buff!!! I know I need a makefile utility
(¿makefile.pl?), but I don’t know what exactly it is and how does it work.
Thanks a lot if you can help me. Sorry for possible disturbances/time
wasted/economical losses/etc etc. Long life for bioperl.

NOTE: I’ve noticed that modules generally aren’t bigger than 100Kb. Should I
search for and install additional modules using the activestate perl package
manager? (I haven’t done it for bioperl because of its size. I have a 56K
modem and sometimes connection is interrupted by phone calls, so I used a
download manager program called Go!zilla).

Antonio Ramos Fernández, Girona, Spain.

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