Augustus new species training

Question

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Hi ! I am trying to train augustus for glycine and I am following the steps you have mentioned.

While using gff2gbSmallDNA.pl, I am getting error Couldn't open gff.

While using autoAug.pl following error:

Error: The environment variable AUGUSTUS_CONFIG_PATH is not define

Can any one help me with this?

Answer 1

[SES]

The error tells you exactly what the problem is, you need to define that variable to point to the "config" directory. For example,

export AUGUSTUS_CONFIG_PATH=/my_path_to_AUGUSTUS/config

If you put that in your shell script before you call the Perl script it will work, as long as you provide the correct arguments (which is not clear from your post).

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Thank you SES ... I have set the config path inside the perl script I have used. Its working fine as of now.

[victorcana1991]

It worked for me:

export AUGUSTUS_CONFIG_PATH=/path/augustus/config export PATH=$PATH: =/path/augustus/bin