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Update README.md
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Addressing second part of #901
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KatharinaHoff authored Dec 19, 2024
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Expand Up @@ -407,18 +407,12 @@ In order to set the environment variable for your current Bash session, type:

Add the above lines to a startup script (e.g. `~/.bashrc`) in order to make it available to all bash sessions.

Perl scripts within GeneMark-ES/ET/EP/ETP are configured with default Perl location at `/usr/bin/perl`.

If you are running GeneMark-ES/ET/EP/ETP in an Anaconda environment (or want to use Perl from the `$PATH` variable for any other reason), modify the shebang of all GeneMark-ES/ET/EP/ETP scripts with the following command located inside GeneMark-ES/ET/EP/ETP folder:

```
perl change_path_in_perl_scripts.pl "/usr/bin/env perl"
```

You can check whether GeneMark-ES/ET/EP is installed properly by running the `check_install.bash` and/or executing examples in `GeneMark-E-tests` directory.

GeneMark-ETP is downward compatible, i.e. it covers the functionality of GeneMark-EP and GeneMark-ET in BRAKER, too.

Warning: installing GeneMark-ETP for BRAKER in conda environments has lead to multiple problems reported by users (Issues!). We can not offer support for conda installations. Please use the singularity image instead.

#### AUGUSTUS

Download AUGUSTUS from its master branch at <https://github.com/Gaius-Augustus/Augustus>. Unpack AUGUSTUS and install AUGUSTUS according to AUGUSTUS `README.TXT`. ***Do not use outdated AUGUSTUS versions from other sources, e.g. Debian package or Bioconda package! BRAKER highly depends in particular on an up-to-date Augustus/scripts directory, and other sources are often lagging behind.***
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