System requirements

Requirements for installation on a UNIX system

Required:

A UNIX machine with a recent version of Perl installed. Perl is free and available for almost all types of UNIX. Perl is available here.
Perl needs the GD, Net::Telnet, LWP, and HTTP modules installed. They are included in the package, but it is better to obtain the latest version from CPAN.
The programs use mail to send and receive BLAST searches, so mail needs to be installed and the mail service turned on.

Optional:

MZEF, an exon prediction program, is used through the service available over the internet, but the mouse exon prediction currently don't work. MZEF can be installed on your local machine if it has SunOS 5.5 or DEC Alpha OSF/1 3.2c (it may run on other versions of these OSes, try it and see). MZEF is included in the package with my programs, and can also be downloaded at the MZEF site.

Not required:

The programs are not CGI, just plain programs.
The programs are text-based, and so X-windows access is not needed.

Requirements for installation on a Mac

A subset of the programs are available on the Mac. The Mac versions of the programs can be useful when used along with full set of programs available on a UNIX machine, but they are of limited utility when used alone.

Required:

A Mac with MacPerl version 5.2.0r4 or later installed. MacPerl is free and available at the MacPerl homesite. MacPerl can be downloaded directly: Download MacPerl.

Instructions for downloading and installing this package

UNIX instructions

Download instructions

Download the gzipped and tarred package: CGAT_0.910.tar.gz

Installation and configuration instructions

Install Perl, version 5 or later if it's not installed on your machine. To check if Perl is installed on a Unix machine, type:

perl -V

Ungzip and untar the CGAT_0.910 package.

ungzip CGAT_0.910.tar.gz
tar xvf CGAT_0.910.tar

If the Perl module GD (GD.pm) is not installed, you will have to compile it. Unzip and untar GD.pm.tar.gz, and follow the directions. To determine if GD is installed, type 'perl -e "use GD"'. If GD is not installed, a message like this will be shown: "Can't locate GD.pm in @INC at -e line 1.".

Add ~/CGAT to your path. (Optional if this will be used by one person, necessary for a multiple user installation, but probably a good idea in any case.)

Install MZEF if desired, and if it can be installed on your machine (available for SunOS 5.5 or DEC Alpha OSF/1 3.2c (it may run on other versions of these OSes, try it and see). Ungzip and untar the MZEF program. MZEF will be placed in a subdirectory of the directory which it is untarred in.

ungzip MZEF.tar.gz
tar xvf MZEF.tar

Read the MZEF installation instructions in the README file. Configure CGAT so it can find MZEF. Under construction. MZEF must be run separately, and the results are then imported into a fplot file using the preplot program.

Install lineplot. Lineplot is provided compiled for SGI 6.2 and SUN 5.6 OSes. You may need to recompile. To do this, unzip and untar the gd library, and follow the instructions to compile it. Then copy the header files to the directory that contains lineplot.c, and use lienplot.compile to compile the program. You may need to set lineplot.compile to use the compiler installed on your computer. lineplot produces 3 warnings when compiled--these are benign.

Configuration instructions

Use the program Perl_set to configure the programs to find Perl on your machine. Perl_set sets the first line of every Perl program to reflect where Perl is located on the computer. If Perl_set doesn't work, you can fiddle with it, or set the first line of every Perl program by hand. The first line should be '/perl_path/perl -I/CGAT_path/CGAT'.
Modify your path to include the directory in which the CGAT programs are located. Typically, the new path is added to the existing 'set path...' command in a initialization file (.cshrc, or .login). You will need to log out and back in for this to take effect.
Before running dna_to_fplot or blast_off, make modifications to blast_off.config specific for your computer. Your email address must be set.
Test the programs.
1. Type 'cutdna -q' to test if the programs can be run. This will produce the help sheet for cutdna, and should take a few seconds.
2. Type 'mask -gtest.repeats test.fasta >test.mask' to test whether Perl can find the modules, and whether mask can access the internet. test.fasta should be a small genomic sequence file. test.repeats will contain a list of repeats, and test.mask will contain masked DNA. This should take a few minutes to run.
3. Type 'dna_to_fplot test.fasta' to run automated analysis on the DNA sequence in file test.fasta. Use a relatively small DNA sequence, say 10 kb. A large number of files will be generated, test.html, test.gif, and test.Legend.html will be the final output files. They can be viewed in a web browser. This will take between a few minutres and several hours to run, depending on network conditions and the load on the BLAST servers.

Read the docs.

Mac instructions

Download instructions

Under construction. Contact Jim Lund at the address below.

Installation and configuration instructions

Install Perl, version 5.2.0r4 or later if it's not installed on your machine.

Unstuff and expand the file containing the package using the free program Stuffit Expander.

Read the docs. To use the Mac programs, generally a file is dropped on the program's icon. If needed, a options window will pop up, and the results will either be written to a file or displayed in the program's window.