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GeneMark Environment Variables
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gm
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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:
DEFMAT=ecoli_4.mat
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
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Variable Name
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Usage
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DEFMAT
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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.
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GMARGS
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This specifies the default arguments to be used by GeneMark. Anything that appears
in GMARGS is prepended to the arguments on the command
line.
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GMBLAST
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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
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GMBLITZ
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This works exactly as GMBLAST above, but is activiated
by using
the -Z optionwill be sent to this address instead. GMBLAST
to GeneMark.
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GMFASTA
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This works exactly as GMBLAST above, but is activiated
by using
the -F optionwill be sent to this address instead. GMBLAST
to GeneMark.
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MATPATH
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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 (':').
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PATH
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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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previous: GeneMark Options
next: GeneMark Matrix Files
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