Installing Genquire for Windows
Unlike Unix/Linux users, Windows users are seldom familiar with
command-line installations, and are unlikely to have any of the support
files Genquire needs pre-installed on their systems. Below is a step-by-step
description of how to obtain these files, and how to install them.
If you have already installed some or all of these files, you are ready
to go directly to the Genquire Documentation for an explanation of how
to configure Genquire for your system. All of these files, including
Genquire, are provided free-of-charge under their respective open-source
license agreements... and users should keep that in mind before writing
nasty emails complaining about installation problems :-)
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Get ActiveState Perl: go to http://www.activestate.com.
Follow the link to Perl under "Solutions", or look under the catagory "Releases"
for the latest version of ActivePerl. This is the package you want
to download. Pick your operating system from the list, and download
the installer. It requires that you have Microsoft Installer on your
system, and tells you how to get it if you don't have it already.
once ActivePerl is installed, you need to start building up your
set of Perl modules. These are available using an ActivePerl program
called "Perl Package Manager" (PPM). Go to a command prompt and type:
c:\> ppm
this will start your PPM program. The prompt becomes "ppm>".
There may be some questions during the install... just answer them if you
know the answer, or leave the defaults.
now we need to start installing modules. The modules we need are:
Tk, Tk-JPEG, DBI, dbd-mysql, LWP, Storable (possibly some others... follow
the same methods as below to get the rest). The way they are installed
is:
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ppm> install term-readkey
... lots of messages... just watch the pretty text scroll up
your screen until it is finished, then...
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ppm> install tk
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ppm> install tk-jpeg
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ppm> install DBI
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ppm> install dbd-mysql
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ppm> install LWP
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ppm> install Storable
Exit from PPM by typing "exit" and pressing enter. You should be
back at yoru normal command prompt now.
Obtain the Windows version of CVS from: http://www.cvshome.org/downloads.html.
Install it, then follow the
following instructions to configure it.
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It's only one file, cvs.exe, so install it somewhere in your PATH (eg.
C:\Windows) to make life easy on yourself.
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drop to your command line and cd until you are in your root (usually C:\)
directory
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C:\> edit autoexec.bat
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at the end of your autoexec.bat, include the following lines:
set HOME=C:
set HOMEDRIVE=C:
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save these changes (as autoexec.bat)
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create a new file called ".cvspass" (yes, include the dot), by typing C:\>
edit .cvspass
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do not enter anything into this file, leave it empty. Just save it,
and exit.
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restart your computer
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go to the command (DOS) prompt again, and type C:\>
cvs
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if you get a bunch of instructions on how to use cvs, then move on, otherwise,
re-check the instructions above.
Now we are going to use CVS to get hold of the latest versions of:
BioPerl-live, bioperl-gui, go-api, and Genquire itself!
GET BIOPERL: Drop back to your command prompt and type:
c:\> mkdir BIO_SUPPORT
c:\> cd BIO_SUPPORT
c:\BIO_SUPPORT> cvs -d :pserver:cvs@cvs.bioperl.org:/home/repository/bioperl login
when prompted, the password is 'cvs'. Then type:
cvs -d :pserver:cvs@cvs.bioperl.org:/home/repository/bioperl checkout bioperl-live
you will get another long stream of stuff, just sit tight, then type:
cvs -d :pserver:cvs@cvs.bioperl.org:/home/repository/bioperl checkout bioperl-gui
and wait again. Congratulations! You have now installed BioPerl.
For more info, visit http://www.bioperl.org
GET GO PERL-API: Now we need to collect the GO perl-api. For
more information on the GO project visit http://www.geneontology.org.
To get the code, type:
cvs -d :pserver:anonymous@cvs.geneontology.sourceforge.net:/cvsroot/geneontology login
when prompted for a password just hit "Enter" - there is no password.
Then type
cvs -z3 -d :pserver:anonymous@cvs.geneontology.sourceforge.net:/cvsroot/geneontology co go-dev
lots of stuff scrolls on your screen again - no worries, this is a good
sign! When it is finished, go to the next step.
Now... Get Genquire! First, log in by typing the following. When
prompted for the password, just press Enter.
cvs -d :pserver:anonymous@bioinformatics.org:/cvsroot login
Then, type the following, making the necessary obvious
substitution for the modulename.
cvs -d :pserver:anonymous@bioinformatics.org:/cvsroot checkout Genquire
NOTE: The code for bioperl, bioperl-gui, and Genquire, are changing
on a daily basis (hopefully for the better!). We encourage users
to update frequently. To update your code, do the following:
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drop to the command prompt
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cd into your BIO_SUPPORT folder (or wherever you put the cvs checkouts)
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there should be three subfolders: bioper-live, bioperl-gui, and Genquire.
cd into each of these subfolders in turn, and type:
cvs update -d
this will update your code with any changes that have been made since your
last update.
Genquire itself needs some configuration to tell it where to find things
on your system. This process is described in the Documentation.html
file, found in your Genquire folder. If you need additional help,
you should write to the Genquire Users mailing list:
genquire-users@bioinformatics.org