Sample Installation Walk-Through for Windows 98 (all-Perl version)
TABLE OF CONTENTS
This page describes the steps we performed to install the PipTools
package on a particular PC running Windows 98. Your mileage may vary,
depending on Windows version, system configuration, other software
installed, etc., but at least this should give you a feel for what
is involved. Also, please note that although these instructions were
accurate at the time they were written, the details tend to become
outdated quickly (e.g., if ActivePerl reorganizes its web site, or
a new version of Boulder becomes available).
We chose to use ActivePerl (plus the Boulder module) to run the tools
written in Perl. This is a popular, high-quality implementation, and
is freely available for download.
Specific folder names are given here for concreteness, but you can
substitute different names if you prefer.
- Create a temporary download folder on your hard drive called, say,
c:\perl.tmp , and another folder where the
software will actually be installed, say c:\perl .
- Go to the
ActivePerl page
and click on Download. Make sure you have all the required software
installed, as listed for your platform. For example, it says that for
Windows 98 you'll need Internet Explorer 5 or higher, and Windows
Installer 2.0 or higher. Unless you're sure you have these already,
follow the links to download and install them.
- Click on the red Next arrow near the bottom right corner of the
screen, and then select the Windows MSI link. When asked, tell Windows
you want to save the file in c:\perl.tmp , rather
than opening it directly from the server.
[Update: as of 20 Apr 2003, you have a choice here between ActivePerl
5.6.1 and ActivePerl 5.8.0; however for Windows, the Boulder PPM module
(see below) is currently only available for the 5.8.0 version of
ActivePerl.]
- Copy the downloaded ActivePerl...msi file to
c:\perl , then run it and follow the instructions
on the screen, keeping the default choices.
- When the installation is complete, a help page will pop up with
Release Notes and other information. You can access this again later
from Start - Programs - ActiveState ActivePerl 5.6 - Documentation, but
you should at least look it over now to familiarize yourself with it.
- The Getting Started section of the Readme page (which is located under
Getting Started in the documentation's outline) explains how to test
the installation using a sample Perl script that is included for this
purpose; try it now to make sure your new Perl interpreter is working.
Note that you must restart your computer (if you didn't already), in
order to make the new path settings take effect so Windows can find
the new programs.
- Eventually you can delete the c:\perl.tmp folder,
once everything is working.
- We had difficulty building the Boulder module directly from its source
code, because the MakeMaker module generated a corrupted Makefile.
(According to listserv postings, this sort of problem is not uncommon
with ActivePerl+Cygwin, and may have something to do with compiler
switch settings.) Fortunately ActiveState provides pre-built versions
of many CPAN modules (including Boulder) which are much easier to install
anyway, thanks to the Perl Package Manager (PPM). The only drawback is
that these may not always be quite up to date, but that probably won't
matter to the PipTools.
- Installing Boulder using PPM is usually very simple. First make sure
you are connected to the internet (e.g., dial your modem). Then type
the following in the MS-DOS Prompt window (it does not matter what the
current directory is):
Note that if your connection uses a firewall or proxy, there are a
few extra steps; please see the PPM, Proxies and Firewalls section
of the Using PPM page (which is located under ActivePerl FAQ in the
ActivePerl documentation's outline) for details.
- Create a folder on your hard drive called, say,
c:\piptools . (We won't use a temporary download
folder this time; this way you'll have the source files to refer to later.)
- Download
piptools-perl.zip into c:\piptools .
- Unzip it, using a program that can handle PKZIP format. Make sure the
subdirectory structure gets recreated (e.g., by using
pkunzip -d ). This will produce a folder named
after the release date of the PipTools version you downloaded (e.g.
piptools-perl.2002-01-16 ) containing all of the
source files and documentation.
- On a Unix system, Perl scripts can be made executable by setting
their execute permissions and including a special line at the top
which tells the Unix shell that in order to run this script, it
should pass it to the program listed on that line, namely the Perl
interpreter. However, Windows does not support this
"#!" syntax, so you need to arrange another way
for the Perl interpreter to get called when you run the tools.
The ActivePerl documentation suggests several workarounds for this
problem, but none of them worked well for us. (Batch file "wrappers"
do not allow redirection of the output to a file, at least on Win98,
and the pl2exe utility is apparently no longer
included in the ActivePerl distribution.) So until we find a better
solution, the simplest thing is to invoke the Perl interpreter
manually by typing perl -S at the beginning of
each PipTools command, as in
| |
perl -S genbank2exons genbank_file > output_file
|
- Make sure the installed program files are in your path, so your
operating system can find them when you try to run them from another
folder. You can do this by adding a new line
| |
SET PATH=c:\piptools\piptools-perl.2002-01-16;%PATH%
|
to the end of your c:\autoexec.bat file. Be
sure to use a plain-text editor like Wordpad or Notepad (not Word!).
You will need to restart your computer for this change to take effect.
- Copies of the PipTools documentation pages (the same ones from our
server) are available in the
c:\piptools\piptools-perl.2002-01-16\docs folder.
- ActivePerl can be uninstalled using the standard Win98 Add/Remove Programs
window (available from Start - Settings - Control Panel). However,
this will leave a few files in your c:\perl folder
(including Boulder), so to remove the Perl stuff completely you'll have
to delete these manually. It may also leave your path set to include
c:\perl\bin ; this shouldn't do any harm, but you can
edit your c:\autoexec.bat file (with Wordpad or
Notepad, not Word!) to remove it if you like.
- To remove the Boulder module without removing ActivePerl, use PPM again:
- To uninstall the PipTools themselves, just delete the
c:\piptools folder and remove the line you added
to your c:\autoexec.bat file.
Cathy Riemer and Matt Weirauch, April 2003