I'm trying to run Braker2 to annotate my genome with the help of RNA-seq data:
braker.pl \ --genome=$ASSEMBLY \ --bam=$RNA_BAM \ --gff3 \ --cores=$THREADS
I get an error:
# Fri Aug 12 18:07:33 2022: ERROR: in file /apps/system/easybuild/software/BRAKER/2.1.6-foss-2019b-Python-3.7.4/scripts/braker.pl at line 1710 AUGUSTUS_CONFIG_PATH/species (in this case /apps/system/easybuild/software/AUGUSTUS/3.3.3-foss-2019b/config/) is not writeable. There are 3 alternative ways to set this variable for braker.pl: a) provide command-line argument --AUGUSTUS_CONFIG_PATH=/your/path b) use an existing environment variable $AUGUSTUS_CONFIG_PATH for setting the environment variable, run export AUGUSTUS_CONFIG_PATH=/your/path in your shell. You may append this to your .bashrc or .profile file in order to make the variable available to all your bash sessions. c) braker.pl can try guessing the location of $AUGUSTUS_CONFIG_PATH from an augustus executable that is available in your $PATH variable. If you try to rely on this option, you can check by typing which augustus in your shell, whether there is an augustus executable in your $PATH Be aware: the $AUGUSTUS_CONFIG_PATH must be writable for braker.pl because braker.pl is a pipeline that optimizes parameters that reside in that directory. This might be problematic in case you are using a system-wide installed augustus installation that resides in a directory that is not writable to you as a user.
Braker2 was kindly installed by someone managing our cluster on my request, but this means I will not have write permissions for the Augustus config. I myself failed with a conda installation of Braker2. Any way to overcome this error with the central installation?
Thanks for any suggestions!