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GeneMark Environment Variables gm

General Information About Environment Variables

Environment variables are a feature of the UNIX environment that permits you to configure your own settings for program features. This can give you great control over the behavior and default options used by programs. You can also modify your login procedure to automatically set up the value of these variables every time you login.

How you set an environment variable will depend on the UNIX shell that you use when you login. To see what shell you are using, type the following at the UNIX prompt:

echo $SHELL

SHELL is an environment variable that indicates the name of the shell (command environment) that you are using. The command ' echo' simply prints out what follows it, and the ' $' symbol tells the shell to replace the word that follows it with the value of the environment variable with that name.

If you are using csh, then you would set an enviroment variable using ' setenv', like so:

setenv DEFMAT ecoli_4.mat

If you are using sh, then you would set an environment variable like so:

export DEFMAT

Most other shells permit you to combine the lines used in the sh case like so:

export DEFMAT=ecoli_4.mat

If you are not familiar with how to setup your login to set environment variables at login, you should contact your system administrator or consult you available documentation.

Environment Variables Recognized by GeneMark

Variable Name Usage
DEFMAT The name of the matrix file to be used by GeneMark if none is specified. i.e., DEFMAT=ecoli_4.mat. This matrix is searched for in the default matrix directory or the list of directories specified by MATPATH.
GMARGS This specifies the default arguments to be used by GeneMark. Anything that appears in GMARGS is prepended to the arguments on the command line.
GMBLAST If this environment variable exists and contains a valid e-mail address (must include the ' @' symbol and machine name) any sequences sent using the -B option may also contain the name of a program or script. If so, GeneMark executes the command line specified in this variable replacing every instance of '%s' with the name of a file containing a sequence in FASTA format. For example:
GMBLAST=/usr/local/bin/blastp nr %s
GMBLITZ This works exactly as GMBLAST above, but is activiated by using the -Z optionwill be sent to this address instead. GMBLAST to GeneMark.
GMFASTA This works exactly as GMBLAST above, but is activiated by using the -F optionwill be sent to this address instead. GMBLAST to GeneMark.
MATPATH The list of directories in which to search for GeneMark models. This takes the same form as the standard UNIX PATH variable, a list of directories seperated by colons (':').
PATH This is not strictly a GeneMark environment variable. This value tells the shell where to look for programs when asked to run one. The GeneMark program files should be in a directory that is listed in this path.

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