Braker is missing JAVA_PATH and others - disable the UTR option in the wrapper

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# Fri Oct 20 14:01:56 2023: Trying to set $PYTHON3_PATH...
# Fri Oct 20 14:01:56 2023: Did not find environment variable $PYTHON3_PATH.
# Fri Oct 20 14:01:56 2023: Trying to guess PYTHON3_PATH from location of python3 executable that is available in your $PATH
# Fri Oct 20 14:01:56 2023: Checking /opt/conda/bin as potential path for $PYTHON3_PATH.
# Fri Oct 20 14:01:56 2023: Success! Setting $PYTHON3_PATH to /opt/conda/bin!
# Fri Oct 20 14:01:56 2023: Trying to set $JAVA_PATH...
# Fri Oct 20 14:01:56 2023: Did not find environment variable $JAVA_PATH.
# Fri Oct 20 14:01:56 2023: ERROR: in file /opt/BRAKER/scripts/braker.pl at line 1795
$JAVA_PATH not set!
There are 3 alternative ways to set JAVA_PATH for
braker.pl:
   a) provide command-line argument --JAVA_PATH=/your/path
   b) use an existing environment variable $JAVA_PATH
      for setting the environment variable, run
           export JAVA_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 
      JAVA_PATH from the location of java
      executable if it is available in your $PATH variable.
      If you try to rely on this option, you can check by
      typing
           which java
      in your shell, whether the executable is in your $PATH

```

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It seems there is no Java installed in this container :(

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Trying now with:

FROM teambraker/braker3:v.1.0.4

RUN conda install openjdk -y

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Ok, that worked. But now we have:

#**********************************************************************************
#                               BRAKER CONFIGURATION                               
#**********************************************************************************
# BRAKER CALL: /opt/BRAKER/scripts/braker.pl --genome /data/dnb09/galaxy_db/files/d/b/d/dataset_dbd4d62f-98c6-458e-b482-c7ccdea68d1c.dat cd --bam /data/dnb09/galaxy_db/files/2/4/2/dataset_2426e895-6b72-4c21-9020-10f5b7021c9a.dat --rounds 5 --UTR=on --species Pm_1 --alternatives-from-evidence=true --gc_probability 0.001 --downsampling_lambda 2 --threads 6 --useexisting --JAVA_PATH=/opt/conda/bin/
# Sat Oct 21 12:43:46 2023: braker.pl version 3.0.3
# Sat Oct 21 12:43:46 2023: Only RNA-Seq input detected, BRAKER will be executed in ET mode (BRAKER1).
# Sat Oct 21 12:43:46 2023: Configuring of BRAKER for using external tools...
# Sat Oct 21 12:43:46 2023: Trying to set $AUGUSTUS_CONFIG_PATH...
# Sat Oct 21 12:43:46 2023: Found environment variable $AUGUSTUS_CONFIG_PATH.
# Sat Oct 21 12:43:46 2023: Checking /usr/share/augustus/config/ as potential path for $AUGUSTUS_CONFIG_PATH.
# Sat Oct 21 12:43:46 2023: Success! Setting $AUGUSTUS_CONFIG_PATH to /usr/share/augustus/config/!
# Sat Oct 21 12:43:46 2023: WARNING: in file /opt/BRAKER/scripts/braker.pl at line 1894
AUGUSTUS_CONFIG_PATH/species (in this case /usr/share/augustus/config//species) is not writeable. BRAKER will try to copy the AUGUSTUS config directory to a writeable location.
sh: 1: Syntax error: Unterminated quoted string
Failed to execute: java -version 2>&1 | grep "openjdk version" | awk -F[".] -v OFS=. '{print $2,$3}' at /opt/BRAKER/scripts/braker.pl line 2299.

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and if this one is solved, I get this one:

# Sun Oct 22 13:19:59 2023: ERROR: in file /opt/BRAKER/scripts/braker.pl at line 1795
$GUSHR_PATH not set!
There are 3 alternative ways to set GUSHR_PATH for
braker.pl:
   a) provide command-line argument --GUSHR_PATH=/your/path
   b) use an existing environment variable $GUSHR_PATH
      for setting the environment variable, run
           export GUSHR_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 
      GUSHR_PATH from the location of gushr.py
      executable if it is available in your $PATH variable.
      If you try to rely on this option, you can check by
      typing
           which gushr.py
      in your shell, whether the executable is in your $PATH

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Oh ... maybe it is because of:

⚠️ The container does not include Java/GUSHR/anything UTR related because we are currently not maintaining UTR prediction with BRAKER. It's buggy and unstable. Do not use it.

I guess we should take out the UTR option for now.

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#39