[Bioperl-l] NT installation guide - RFC

Tue, 13 Mar 2001 11:17:02 +0100

# Unless anyone objects (or unless Mathieu is quicker), I will send
# an (ascii) version to the list tomorrow morning (CET).

Here goes. Feel free to tear into it.
--------------------------------------------------------------------------------
--------
Installing Bioperl 0.7 on Windows NT 4.0 running ActivePerl 5.6

Disclaimer

I could play the part of a bio-informatician and of a perl programmer on TV.
However,
I'm not intimately familiar with either WinNT or Bioperl. Also, I haven't
actually used
bioperl on this machine (or much at all) at the time of this writing. Caveat
emptor.

Tools

Most perl modules are distributed tarred and gzipped, so you will need a program
that can
handle compressed files. WinZip (www.winzip.com) works nicely for me.
You will also need a make utility. Nmake seems to be the tool of choice, and is
freely
available (http://download.microsoft.com/download/vc15/Patch/1.52/W95/EN-
US/Nmake15.exe). Executing this self-extracting program generates the files
readme.txt,
nmake.err and nmake.exe. You can copy nmake.exe and nmake.err to a directory on
your
path, such as C:\WINNT\system32\, or you can copy these two files into the
directories
from which you wil install bioperl and its dependencies.
To verify which directories constitute your path, you can open a command prompt
(a
"DOS-box") from the start menu, and use the command 'path'. Don't close that
window
yet, we will need it.

Installing ActivePerl

A more or less up-to-date version of Perl for Windows is going to be necessary.
The
current release is perl 5.6 (build 623). Perl 5.005 should be fine; 5.004 will
lack part of
the functionality. If somehow your NT has Perl 5.003 or earlier installed, all
bets are off.
A Perl installation is freely available from ActiveState
(http://www.activestate.com/Products/ActivePerl/Download.html. I used
http://www.activestate.com/download/ActivePerl/Windows/5.6/ActivePerl-5.6.0.623-
MSWin32-x86-multi-thread.msi, but this link is likely to change in the near
future).
You will need Windows Installer 1.1 to use this binary file.
(http://www.activestate.com/download/contrib/Microsoft/NT/InstMsi.exe)
If this tool is installed, doubleclicking on the .msi file you downloaded will
start the
installation process.
I chose a full installation (including examples, docs and scripting), and
elected to have
my path modified and a .pl file association created. For some reason, the setup
program
never asked for a path, but installed to E:\Perl; your mileage may vary. Note
that the only
entry in you Start Menu is a shortcut to the (lovely) documentation.

Dependencies for Bioperl

A full list is provided in http://bioperl.org/Core/external.shtml, as well as in
http://bioperl.org/Core/POD/bptutorial.html.

External packages

I haven't tried to install the external packages (AceDB, Blast, Clustalw,
Tcoffee), or the
XS based modules from bioperl-ext.

Perl modules

The remaining dependencies are perl modules. The dependencies page mentioned
Bundle::Bioperl, but I found it quick and easy to install the modules one by
one. Some of
these (LWP and its dependencies, and XML::Parser) are included in the ActivePerl
installation. This also implies you shouldn't worry about 'xpat'.
Most of the remaining prerequisites can be installed using PPM, the Perl Package
Manager. (When you installed ActivePerl, you also installed the full
documentation for
perl and the ActiveState additions. The paragraphs on PPM are worthwhile.
Basically,
PPM is CPAN.pm for Windows.) The following supposes your NT is connected to the
Net.

Start PPM by typing 'ppm' at the command prompt (but doubleclicking
Perl\bin\ppm.pl
works as well). This gets you the 'PPM> ' prompt. You can now issue the
following
commands:
install File-Temp
install IO-String
install IO-stringy
install XML-Writer

You will be asked to confirm each install command.

Two final modules don't have an ActiveState port at the time of this writing.
However, as
both are pure perl modules, it is easy to install the CPAN versions.

o	libxml
Download http://www.cpan.org/modules/by-module/XML/libxml-perl-0.07.tar.gz.
(You might verify whether there is a more recent version using
http://search.cpan.org).
Extract this archive to a temporary directory. At a command prompt, change
directories
to the location where you expanded the archive, and issue the following
commands:
perl Makefile.pl
nmake
nmake test         (This will generate a warning 'uninitialised variable', but
will result
                           in 'All tests successful'.)
nmake install

o	XML::Node
Download http://www.cpan.org/modules/by-module/XML/CHANG-LIU/XML-Node-
0.10.tar.gz. (You might verify whether there is a more recent version using
http://search.cpan.org). Extract this archive to a temporary directory. (The
distribution
contains a file XML::Node.sgml, which you will not be able to extract. You can
safely
ignore that, as long as the other files are extracted.) At a command prompt,
change
directories to the location where you expanded the archive, and issue the
following
commands:
perl Makefile.pl   (will complain about the missing .sgml file; ignore)
nmake
nmake test           (should give some output, interspersed with 'ok1', 'ok2'
and 'ok3')
nmake install

Bioperl

You can find the latest release at http://bioperl.org/Core/Latest/index.shtml.
Download either the tar.gz file or the .zip file, and expand to a temporary
directory. At a
command prompt, change directories to the location where you expanded the
archive, and
issue the following commands:
o	perl Makefile.pl
This warns that Bio::DB::Ace is going to be useless without additional external
modules.
It also generates the mysterious message 'Generated sub tests. go make
show_tests to see
available subtests' to stderr. Nmake show_tests does little for me, though.

o	Nmake
This will simply set up the directory structure for testing and installing.

o	Nmake test
This will generate lots of output, mostly just of the form
't\AAChange..........ok'.
Highlights include:
@	skipped tests for Blast
@	problems in File::Temp when testing Bpsilite
@	skipped tests for Clustalw, with an URL
@	(possibly) skipped tests for DB, if the test script finds your connection to
the
Net is down or too slow.
@	unidentified values and failed tests for GDB
@	an exception and failed tests for Index
@	skipped tests for SearchDist, StandAloneBlast and Tcoffee.
(skipped tests are due to external programs not being installed.)

And the final summary on my machine is:
Failed 2/60 test scripts, 96.67% okay. 16/953 subtests failed, 98.32% okay.
24 subtests skipped.

Unfortunately, nmake does not exit graciously at all:
NMAKE : fatal error U1077: 'C:\WINNT\system32\cmd.exe' : return code '0xff'

o	Nmake install
This will copy the modules to your perl\site\lib\ hierarchy, so they are
available for
inclusion in your scripts.
--------------------------------------------------------------------------------
--------

--
Jurgen Pletinckx
Algonomics NV